In the beginning scene where Salvor and her father are sitting on the bench, it appears that the father put his hand over Salvor's shoulder, but as the camera switches back and forth to the other angle, his hand is on the bench and not on Salvor's shoulder.
Colour blindness doesn't make objects invisible or transparent, it just makes certain colours indistinguishable. Brother Day would still have seen the red birds. In the image where they are revealed they are an addition over the top of the previous shot.
It makes absolutely no sense for the Thespin fighters to leave their ships when they get to Terminus. They have total control of the battlefield from the air. By leaving them they surrender all control to one pilot who could easily just be shot by the Anachreons to win the battle. They've also lost contact with one their fighters and know that the enemy leader is missing. They would surely have connected those two events and known she was coming.
As the null field turns off a flock of birds is shown resuming their flight over the vault. The field didn't affect gravity though as all the people in it's area fell over so the birds should all be on the ground and probably dead from the fall.