Deliberate mistake: When Jack fights the impostor, they are roughly the same height, but when the impostor is revealed to be Angelica, she is suddenly much shorter than him. (00:21:30 - 00:23:50)
Deliberate mistake: In the scene where they break into the train from its roof, you can notice that despite the high speed and the consistent wind, Captain America's fellows have no difficulties in running, standing up still, and even jumping, like they felt no air resistance. Moreover, you can see that their hair is not moving at all, completely missing to realize any "windy" effect.
Deliberate mistake: In the opening title sequence, just after the title of the movie is shown, Puss cuts a P with his sabre into a curtain or flag. In the middle of the P, there is cloth remaining, but since he cuts edges all around this to make the Capital P, this cloth should fall away as it is no longer attached to anything, yet it floats in mid air.