Deliberate mistake: After Peter says, "We can't both have her lady," he shuts the window from the outside and the bottom pane is placed on the outside of the top stained glass pane. This is obviously done specifically for this shot so Peter would be able to shut the window and try to keep the Darlings from opening it. However, in the next shot as the Darlings succeed in opening the 'stuck' window, the bottom pane is on the inside of the top stained glass pane. (00:02:05 - 00:58:45)
Deliberate mistake: Towards the end of the movie fish are seen to swim down in order to submerge the net in which they have been caught. Although the attempt seems logical, it actually needs power against the net to push it down. None of the fish seem to touch the net at the bottom however and if it is the whole mass of fish achieving it, then the bottom fish should have been squashed against the net which (again) isn't the case. 'What brings the net down?' is the question here. (Done deliberately by Disney/Pixar to be visually aesthetically pleasing.)
Deliberate mistake: After the game has entered the real world, and Floop and Minion are there to "save the day", Carmen and Juni throws seven pairs of glasses to them. But afterwords, we see there are only four pairs of glasses on Minion and one pair on Floop, which totals five. (01:11:10)
Deliberate mistake: When Kate Barlow shoots the Sheriff, she shoots him between the eyes, but when she kisses him there is no hole or anything on his face.
Deliberate mistake: In the orphanage scene, Santa's bag drops dead center in the fireplace. The noise of the impact gets baby Buddy's attention in a quick shot, and the camera shifts back to the fireplace. Now, the bag has shifted to the viewer's left when Santa's boots are coming down. The shift of the bag is presumably to make room for the boots coming down the chimney.
Deliberate mistake: When Leota is in the front seat of the automobile, the air bag is still full. Air bags will deploy and then immediately deflate to prevent people (or women in crystal balls) from being trapped. (01:10:45)