Continuity mistake: When the boy touches Peter's face, Peter is kneeling and is slightly taller than the kid. Then he says "Here you are, Peter!", the angle swaps to a wide one where Peter is now in a lower position than the kid. Then back to the close-up and he is back to a higher position. The boy's hands are also always inconsistent between the front and side angles.
Continuity mistake: Peter picks up a wooden spoon and flicks imaginary food at Rufio. Looking at Rufio, a black plastic spoon covered in blue flicks some blue and red substance at him that has a consistency if pudding. When Peter looks at the now-covered spoon, it has red, green, yellow and blue stuff stuck on it.
Continuity mistake: At the end of the movie when Peter crawls into Nana's doghouse to greet her (after returning from Neverland) he shakes the doghouse a little as he crawls in, causing snow to fall of its roof, which lands in the two dogbowls next to it. But in the next shot the dogbowls are now empty with no snow in them and also there is a long bone sticking out one of the bowls too. (02:06:20)