@Background Pony #46D8  
She could then freeze Fluttershy while the others tie her up. They could have collected other apples and squished them to get the smell.
 
This whole big apple thing was just annoying. It’s unnatural (even a world of magic has its laws of nature), it’s out of nowhere, it only serves to show how loyal Rainbow Dash Applejack is. – Then the stupid ending with Fluttershy’s fang; this whole episode is just a mess.

Magic requires concentration, this is seen multiple times throughout the show. As powerful as Twilight is now, it’s unlikely she could freeze Fluttershy in place and cure her at the same time. Also, the apple was just the bait to lure Fluttershy to that location so they can use the mirrors to confuse her then-animal-like mind.

@Vaidelot  
I watch a show for it’s story and characters; but if the story or characters has flaws, I can’t enjoy it. Sure, one issue here and there is fine … but this whole episode is filled with tons of them.  
I think the show started going downhill during the course of season 2 … and season 3 was just … meh. And now I have only wached the first 10 episodes of season 6 … still haven’t watched the rest.
 
I’m for a G5, a refresh … as long as it isn’t brony-stuff.  
Too much fan shoutout … it’s annoying =/

@Liggliluff  
She could, but Flutterbat could also rip from her grasp, probably leaving half of her tail behind. And I don’t think Twilight would have risked to injure her crazed friend (who has gone crazy because of her spell in the first place).  
Unfortunately, yes, there are some logical flaws in the show. But usually the overall writing is good enough for people to ignore most of them.

@Vaidelot  
She could yank Flutterbat’s tail.
 
After Twilight froze several adult ponies twice, both times with all ponies at the same time … I would say she’s very powerful. – But sure, they might have been taken by surprise and didn’t show any struggling.
 
But the issue with Twilight (and the writers/animators) is that she’s stupid. She can collect all apples from 10+ trees (S1E4), but didn’t do so in the competition where Applejack’s farm was in danger (S2E15)
 
Flim and Flam allowed the whole Canterlot to help; so she should have written to Celestia and said they needed her help to save Applejack’s farm.
 
But that episode was stupid as Applejack agreed on a deal where she had barely anything to gain, and something huge to lose. …and Flim Flam still owns that farm legally… but they did kinda abandoned it.

@Liggliluff  
Actually, she never froze RD per se… She more or less just used telekinesis to yank on her tail, the same way AJ did with her mouth. The only time she actually used telekinesis to fully control adult pony’s body was in “Green is not your color” with said pony (Fluttershy) being cooperative. Starlight used telekinesis to stop filly Dash but, again, the only time she attempted it on adult pony was already brainwashed Pinkie Pie in “Every little thing she does”. So I believe it’s safe to assume that fully grown pony could, with some struggle, break free from unicorn’s telekinetic spell. Twi is pretty powerful, I give it to her, but not completely OP. But yes, some refreshment would be pretty good since show did started to decline after season 5…

@Vaidelot  
I must remember if she’s frozen more stuff…  
Bats, parasprites, …I know, Rainbow Dash multiple times.
 
Personally; I think Twilight is just too powerful. The show is over, we need new characters. G4.5/G5 please? =|

@Liggliluff  
The projectiles flying in predictable ballistic trajectories, so it’s not a problem for something as smart as Twilight to calculate the necessary lead. Whereas flying creatures move unpredictably and could actively evade.

@sumbozo  
Overthinking can be fun; and this isn’t overthinking … that apple-thing was plain stupid.
 
@Vaidelot  
She managed to freeze missiles in that episode too, so one flying creature shouldn’t be hard.
 
I do agree on the crystal spell; she might have learned it later, and she’s still bad at aiming.

This particular freezing spell (as we could see both in Castle-mania and the episode with feuding families) is areal and takes some time to cast, so it would be pretty useless against fast-moving and actively evading target. Crystal-encasing spell from the season 5 finale would be more useful, but Twi still didn’t know it back there (besides, she had troubles hitting even slowly levitating Starlight with it, let alone something that moves so fast even Dash couldn’t effectively subdue her).

 
Even he would call this overthinking!

The big apple felt very out of universe, as they’ve tried to make stuff “behave natrually”, kinda.  
There was absolutely no need to sacrifise it, as they instead could gather other apples and use them as lures.  
…and how was she able to keep only the big apple?
 
Twilight’s limit of her magic is very random. She can do incredible stuff like… freezing several poines as shown above; or moving a huge amount of apples (S1E4); changing mental behaviour of creatures (S1E10); having a “fix everything”-spell (S2E1); shooting lasers (S2E26) … all with ese.
 
But teleporting several poines a long distance (S2E21); moving an Ursa Minor (S1E6); changing age (S3E5); reverting black magic (S4E23) … requires a lot of magic.
 
Help me fill out this list XD

Just another part of the “AJ must make a sacrifice in this episode because she is the one in the wrong even though she has a completely valid point” aspect of the episode.