Major goof?

Emily, the girl who got kicked out for being too fat. Remember, at the end when Jonathan wants to see all the girls after the workshop performance, emily comes out of her meeting with Jonathan crying and all the other girls rush up to her and asked her what he said to her. Obviously, he was quite pissed about it!

I noticed Anna in the corps in Cooper's ballet immediatly to the right of Sergei and Eva during the final bow, when she said clearly she was the lead in a different ballet when she was talking to her mom on the phone. I always assumed she had done both since they could have been hours apart

That has always bothered me. Considering Emiliy left in the last few weeks and would have had to be replaced as well, I am guessing an understudy was worded up by Eva?

I always thought the girl that was crying was the one at the start of Anna's ballet (I think) who asked Juliet "Are there really only three places?"

I think the corps in JOnathon's ballet were actually professional dancers, so I doubt that Anna was in there (but I have it recorded so I will check)

I just watched the movie again this weekend and thought the same thing. I'm thinking it was the understudy because Eva's original partner (dark-haired guy) is in costume. He even stands by Eva as Sergei tells her "I'm gonna kill you" jokinly when he confronts her about not being told about the switch. I imagine Emily's understudy took her place also.

there had to have been an understudy or swing.

It's not unusual for a corps de ballet dancer to be given an opportunity to dance a soloist role, and sometimes even a principal role. If that were to happen, there would always be another corps dancer to take her place in the ensemble.