“Oops. Well… It’s not like she would have to use her wings. Right?”

Dangerous Mission Outfit
 
is the mission

Not like Fluttershy ever uses them to any real effect anyways.

I.S.S

That mission outfit is just plain dangerous, isn’t it?

Wings are counter-revolutionary!

+1 respect for Rarity.  
Trixie has moved down to 8th place.  
Rarity has advanced to 7th place.

While we can think many excuses (be it Flutter’s dislike of flying, force her to use the ground and not become a highly visible target, etc)the bunny ears make me think Rarity just designed this suit just because Shy would look cute on it…
 
Of course, it’s also practical and accomplished it’s purpose, but yeah I think she was going for cute.

It’s a disguise, now she look like Posey in a bunny ear hoodie. See? Worked like a charm.

Seeing how this dangerous mission outfit is more like a bunny disguise, it would be suspicious if her wings would be left in sight…

I was going to say Rarity made it in a hurry, but I like the other excuses better.

Those birds are holding her up by her hair. That must hurt like a bitch.

Oh Rarity, you devious dame.

As mentioned, Fluttershy’s wings tend to lock up at the first sign of danger.
 
Actually, I think that they had already locked while Rarity was fitting her for the outfit, so she just didn’t bother to cut out holes.

Not a huge mistake, she can’t fly very well to begin with.

A little oversight. Nothing too drastic.

It’s a bunny disguise. A bunny with wings would arouse suspicion.

For her own safety. Can’t have this happening again:
 

Why, it’s so she can’t fly away ofcourse.