I think this conversation here is a good and sad example how many bronies don’t take My Little Pony: Friendship is Magic really seriously, even after all these years and all we’ve seen…..  
When you put a lot of thoughts into something and do an effort to closely analyze something seen in the show and put together the clues to predict a future event, then you are deemed the weird one, while everyone who doesn’t pay attention and just shrugs something off as unimportant background event is most definitely in the right.  
Guess I now know why this fandom does so little actual analyzing…..
 
 
@TyrannisUmbra
 
Anyway, your points are very good and make sense all around. Once the Finale rolls around, we’ll be more convincing with this.  
The fandom needs more members like you!

@TyrannisUmbra  
Then there’s really no way to convince you. Believe what you’d like, but really like Fwelin said; you’re creating way too many details on your own from one blurred image which is actually just very basic foreshadowing. This is a child’s show still, and if an important event is going to be happening then they would show it instead of hide it from the audience.

@ShareMyShipment  
I’ve already addressed what you’ve said before, but I’ll re-iterate:
 
Chrysalis hasn’t been around to see an existing crib. There is no way or reason for her to make a complete duplicate of a crib.  
I’ve said it may be a different carrier, but also, I’ve already said that the one we see in the show isn’t in The Crystalling. At all. We only see it in episode 16. Maybe… a gift from an appreciative Crystal Pony (read: changeling in disguise)?
 
—Actually, this is also confirmed during said episode. When Spike first encounters this changeling, the following conversation comes to play:  
And you’re just ignoring where I said Thorax isn’t exactly a trustworthy source. Changelings are known for deception.  
Not to mention this: “If you look closely, the backplate… is dark. It’s not light blue. The light blue you can see are the wings. This is an entirely different changeling altogether.”

@CMC Scootaloo  
You clearly haven’t read my last point. It’s basically saying “hey, I’m that changeling in the background”. :|  
If that doesn’t convince either of you, nothing will and there’s no point in arguing. It’s clear as day.

@Background Pony #925F  

 
You’re putting way too much thought into a few second, tiny, grainy image that the animators put in as a subtle foreshadowing for Thorax.

@TyrannisUmbra
 
This also lets me think of something else I noticed when watching the Opener, but didn’t mention anywhere, because I thought it doesn’t hold enough significance:
 
After seeing the changeling at the end of the episode, I was thinking that maybe a pony was replaced already, so I rewatched the episode with close attention, stopped every time when ponies were in the background and checked them.  
I mostly did this because I suspected that Shining Armor got replaced, upon noticing a strange, blue tinge in his eyes (which I then found out was always in his eyes except for in the Season 2 Finale, when checking his earlier appearances in the show, so I was wrong with that), but I also checked other ponies while I was at it.  
And there was one mare, only one, who was there twice. All the other background ponies were completely unique. I could dismiss that they just duplicated pony models after animating them to fill the background, because they don’t really do this anymore nowadays and because it was really only just this one mare.  
So I suspected one of them to be a changeling in disguise. But I did not follow the thought further because it didn’t seem like enough evidence to me.  
Now, though….. Things are different.  
The changeling who turned into this mare is clearly Thorax.
 
 
And don’t bother with convincing ShareMyShipment anymore. Some will always be sceptical, no matter what you say, and you brought more than enough better arguments for your observation than her and you don’t have to convince everyone.

@TyrannisUmbra  
“I’m saying it may have been brought in with the changeling meant to take her place.”  
 
Chrysalis hasn’t been around to see an existing crib. There is no way or reason for her to make a complete duplicate of a crib.
 
I’m just going to end this unavailing and pointless argument with this:  
Having something very subtle with no focus at all in the background is a very common way to give hints to the viewers for those who pay close attention. This here may have been an example of them hinting about the upcoming episode “The Times They are a Changeling”. –Actually, this is also confirmed during said episode. When Spike first encounters this changeling, the following conversation comes to play:
 
CHANGELING: “I was part of the attack in Canterlot during the royal wedding, but I had never seen true friendship like that and I couldn’t just steal it and feed off of it’s love. I wanted to share it.”
 
CHANGELING: “After that, I knew I couldn’t live with my kind anymore. I set off looking for love to share, but…”
 
SPIKE: “But what?”
 
CHANGELING: “I’M STARVING! And there’s so much love in the Crystal Empire right now, it’s what drew me here! But it’s driving me crazy!”
 
SPIKE: “That would be from the royal Crystaling.”
 
–  
I’ll leave you to connect the dots from here.

@TyrannisUmbra
 
You’re on to something here, you know that? That fits together way too perfectly for a coincidence or an oddly-shaped changeling leg, or whatever…..  
I’m happy that I’m not the only one who does such deep analyzis of the show. That’s rare in the fandom.  
I’m almost a bit jealous that you found this out. I was so busy with worrying about it that Thorax is a spy and going to fillynap Flurry Heart and bringing her to Chrysalis that I didn’t notice the hints for it that she isn’t the same anymore (see my comment below).  
Now that I think about it, I believe her behavior is also different now. I have to check this again…..  
It’s just now that I realize that I had a weird feeling while watching the episode when seeing her, something that wasn’t there when watching the Opener and that felt like I don’t love her as much as before anymore, which I didn’t wanted to believe, so I shoved that thought away and didn’t pay anymore attention to the feeling. Realizing now where this feeling came from gives me shudders…..  
Also, I’m glad to see that I’m not the only one who doesn’t trust Thorax. The light-blue backplate can mean that he is one of Chrysalis’ top agents, directly below her in the hierarchy of the hive.  
And if you would be Chrysalis, who else would you send for such a crucial mission, if not your best changeling?

You’re right, this makes way too much sense…..  
Of course it can’t be that he was already carrying Flurry Heart in her crib there. This was when he was just flying into the Crystal Empire, after all.  
But here’s the thing:
 
The crib he was holding there wasn’t Flurry Heart’s crib, it was another crib with a young changeling larva. A larva meant to replace Flurry Heart.  
Now what did Twilight hear from Shining Armor and Cadance? That Flurry Heart has grown so much in such a short time. Which Twilight could later confirm. And Flurry Heart didn’t sneeze anymore…..  
So, yeah, Flurry Heart’s replaced already. Thorax replaced her with the changeling larva, then he most likely hoofed Flurry Heart to another changeling who brought her back to Chrysalis with him.  
And the changeling larva happened to be bigger than Flurry Heart and is not skilled enough yet to change its size when transforming, so it kept this size when it turned into Flurry Heart. And of course the changeling larva doesn’t have the same cold/allergy that Flurry Heart has…..  
And after Flurry Heart was gone, Thorax stayed in the Empire for some reason, maybe to do preparations for an invasion.  
Which is as good as explanation why he used the opportunity to get easy access into the Crystal Empire as the one about him planning to fillynap Flurry Heart and taking her with him…..  
This is not Flurry Heart anymore who we see in this episode.

@ShareMyShipment  
The crib was new to e16. It wasn’t in the Crystalling. I’m saying it may have been brought in with the changeling meant to take her place.
 
You cannot see both legs. The ‘top’ one is the tail.  

 
Worth noting, the “blue” on the belly is because of the way the wings are animated, as seen on some of the changelings in this picture (You can see some of them have 4 or more wings while flying, to show movement):  

 
Animation assets are used in side-on shots all the time. Not to mention, when you’re making something SO small, being side-on helps much more with how it looks. Not to mention the shot where the changeling was seen was in the far distance, moving from left to right, pretty much straight on toward the Empire. The profile you’re proposing just doesn’t make sense for the situation, and makes the changeling look deformed. (Front legs way bigger than back, different legs being connected in the wrong place and being different shapes, head in the wrong place, etc)
 
If you want to nitpick about the color, it could have been a different carrier. The SHAPE is what matters.
 
A more ‘apt’ comparison as you said it would be, ‘I have money I made at my neighbor’s expense, in such a way that he would likely want my revenge. The paycheck just came in the mail and I threw a HUGE party to celebrate. My neighbor is probably pissed off and wants to get even with me, and what better way than to come take my money while I’m distracted?’
 
The point that I was making is that it’s way more than just circumstance at work here. There is REAL motive for this to happen, and the fact that a changeling was confirmed means that 1: this was an intended sight, and 2: the writers are thinking of changelings when writing these episodes. I am NOT saying ‘there is a changeling so he did bad things’. I am saying ‘there is a changeling so it’s not unrealistic to expect more of them from the writers this season’.
 
There’s also precedent – In every season premiere since season 3, there has been something which was shown, or referenced, which makes a return in the finale of that season. For S3, it was the journal. For S4, it was the box. For S5, it was Glimglam herself and her idea of the perfect utopia. For S6, what do we have? We have the baby, and we have an easily missed changeling, shown in the last few seconds of the premiere in much the same way S3’s journal was shown.
 
Aaaand lastly, changelings are known for deception. Who says Thorax isn’t still working for Chrysalis? If I was her, I’d have started thinking of ways I could trick the ponies who defeated me into letting their guard down. And like I said before, the swap may not have been made yet.
 
And, here’s a fun fact that I just noticed while checking screenshots just now. There are only two changelings we’ve ever seen with the light blue chitin on their back. The first being Thorax… and the second being Chrysalis herself. And this actually puts the final nail in the coffin about the theory that this changeling is Thorax. If you look closely, the backplate… is dark. It’s not light blue. The light blue you can see are the wings. This is an entirely different changeling altogether.

@TyrannisUmbra  
How do they have the crib if they’re on their way to kidnap?
 
You can see both legs and is indeed dark grey.  

 
Saying the crib is “shadowed” is taking a theory a little too far, and is a start with just you making up details. What you’ve traced as a crib is VERY small and 2 dimensional. Professional animators don’t make props like that completely 2D, and follow with consistent colors.
 
At this point, I can’t tell whether you’re being serious or trolling. Saying the baby is important and seeing a changeling flying nearby does not mean the changeling kidnnapped the baby. That’s just like me saying I have money, a black guy is my neighbor, so he must want to steal my money. It just doesn’t add up.
 
You saying the baby is a changeling doesn’t add up either with the “good changeling” reacting to it.

@ShareMyShipment  
Heading toward the castle with a changeling already transformed and ready to take Flurry’s place. The baby we see in the future is possibly the changeling taking her place (or maybe the swap hasn’t even been made yet).
 
Also, you can’t see both hindlegs. You see one hindleg and the tail. The crib could be gray because it’s shadowed – if it was colored different it would be too obvious. Not to mention the eyes are clearly pointing DOWN. This changeling is looking down toward whatever this unknown ‘mass’ is (and not in the direction it is flying). If it was a leg, that would mean that it was connected to the stomach (and also a completely different shape from the first leg, which is connected to the shoulder and not the stomach)
 
A lot of people seem to be missing the point. The point is just like@Background Pony #8702 says – There is legitimate reason Chrysalis would want to do this. Changelings have been confirmed in the Crystal Empire, so this was not a fluke. The baby is clearly very important, and a possible source for a HUGE amount of love, not to mention that Chrysalis would want to get back at Cadance and Shining. And as was said, it also has /mythology/ reasons behind it, as well.

The theory doesn’t really make any sense. The changeling is headed for the castle, not away, the mistake baby is fine in future episode(s), and what your tracing to be the crib is dark grey with not a single hint of purple, pink, or gold. This is clearly a leg. The changeling is in an average fly position with its arms and legs stretched out, and is in an upper 3Q angle to the camera. You are able to see both of the changeling’s hind legs, and is the same for the front.

historically changelings were the replacements left when fae kidnap babies..

@Stotter  

 
Since when is the second front leg connected to the body via the stomach? Not to mention the shape doesn’t match the shape of a leg.
 
It also seems to be looking /down/ at what it’s holding. When was the last time you looked down at something you’re holding? Maybe, when you’re worried about dropping it? Or worried about dropping something /inside/ it?
 
The shape is pretty perfect. The animators wouldn’t half-ass something like this if it was relevant to anything at all (And judging from the fact that we now have at least one changeling confirmed to be within the Crystal Empire, I’d say this is very, very relevant).
 
Plus, if you were Chrysalis, what would be the best way to get back at Cadance and Shining? Maybe… by doing something to their baby? Replacing and kidnapping sounds like a pretty changeling thing to be doing.

Clearly just the other front leg.

Graspin’ at straws aren’t ya.