The episodes could be aired out of order. After Scootaloo getting noticed by Rainbow Dash in ‘Sleepless’, having Scootaloo not in the next episode was a bit distracting, continuity-wise. Just having her in the background, waving goodbye to RD would have been enough. Replacing Pinkie Pie with Scootaloo would have been even better (the behaviour patterns were pretty much the same).
 
Having Scootaloo suddenly feel surprised, betrayed and abandoned is just not right. Assuming this whole academy-thing takes place after ‘Sleepless’, we can assume that Scootaloo hangs out more with RD than usual (terrifying thought, I know) and as we know, RD is kind of a bragger. If we count in previous episodes, Scootaloo is the head of RD’s fanclub. Point is, Scootaloo would have known that Rainbow would go to the academy and would even know how long it would last: A single week. Any normal pony, like the mane four, would accept that and move on with their lifes. Pinkie did not, but then again, she’s crazy for coco-puffs, so that doesn’t count (once again, replacing her with Scootaloo would have been spot-on).
 
Now to this comic: Having her get the letter and leaving the next day is a bit unrealistic, especially if it would be permanent. You would expect the Wonderbolts to give their new recruits a bit of time to get their things in order before leaving. And once again, if Scootaloo hangs out more with RD, she would have known abaout the academy. She would have known that Rainbow Dash applied and she would have known when the academy starts (Those dates usually are realeased beforehand, especially to those who apply). And Rainbow Dash, assuming she had learned her lesson from season 1, would have not promised Scootaloo to train her on that day, knowing that she might not be there and would have Scootaloo told the reason why (Then again, everypony can make mistakes, so, yeah…). As for Scootaloo, I can see the psychological trauma here: On one hand, she is obsessed with Rainbow Dash and her talent, so seeing her being accepted into the Wonderbolts would make her happy, as it proves what she has been telling everpony she ever met: That Rainbow Dash is the perfect flyer Equestria has ever known in existance, past present and future. On the other hand Scootaloo has become dellusional with Rainbow Dash as her mother/sister/-figure (more than RD really is), so her leaving would of course cause abandoning issues.
 
However, all this is not really shown very well in this comic and these psychological issues would hardly been explored in the actual show (kid’s show and all that), and Rainbow Dash permanently leaving Ponyville is also unlikely (except maybe in a spin-off), so the best course of action would be to assume the episodes were aired out of order…

Why does everyone think she’s gone away permanently after she’s been accepted into the Wonderbolts? I mean, she literally* says “See you in a week!” then flies off, she isn’t leaving forever. She’s only gone for a week, and at least halfway through it the other five give her a care package (after a hurricane attack, but still). So at most she’s gone after days after the end of the episode, which takes a week to air a new one! Of course she’s gonna be back.
 
*as in, the literal term. I’m not being some fool using “literally” as a throwaway word, I’m being serious with the actual term of the word here.

Sooooo Wonderbolts Academy was a fever dream?

Wonderbolts Academy seems out of place anyway. After that she’s back in Ponyville. Why do you think the ending was out in the open. There really is no true ending to that episode.

Scootabuse sucks.  
Im more of a Dashabuse type.

@Bristle_Brew
 
Do I really need to say it? That idiot with the scootabuse obsession.

Wasn’t it confirmed that the episode was played out of order too, meaning she didn’t leave just after the Scootaloo episode?

@Slayer  
Which one?

@Background Pony
 
GET A LIFE!

Great to see RD has her priorities right.

WELP that turn noncannon since she seen in ponyville