(at around 9 mins) When the Man in the Moon communicates to North to identify Jack as the new Guardian, the moon is full. One day later when viewing the moon from North's home (at around 22 mins), the moon is 3/4 full. Way too much has disappeared over a period of 24 hours.
(at around 13 mins) When Jack takes Jamie on a sled ride through town, Jamie passes by the park two times.
(at around 1h 24 mins) When Tooth punches Pitch near the end, there are five tooth fairies hovering by her shoulder. However, the scene switches and she is not shown for a moment. When the scene switches back, only one tooth fairy, presumably Baby Tooth, is with her. As the scene continues, the number of fairies with her continues to change, first to eight, then to none, then back to five.
Every tooth collected by the Tooth Fairy has roots, like a pulled adult tooth, but most of the teeth are supposed to be baby teeth, those that have wiggled loose after being displaced by permanent ones. They should be hollow shells without roots.
(at around 52 mins) While preparing for Easter at the warren, Bunny announces that "There will be springtime on every continent!" Easter only coincides with springtime in the Northern Hemisphere- in the Southern Hemisphere, the holiday coincides with the start of the autumn season instead.
(at around 54 mins) Jack Frost should not be able to carry Sophie home since it was ambiguous as to whether or not she believed in him, and was shown in the beginning of the film that he simply vaporized through his non-believers.
(at around 11 mins) When talking about the egg hunt, Jamie and his friends say it's on Sunday. However, on the banners in the street, visible when Jack and Sandman are talking to Pitch (at around 44 mins), it says that the egg hunt is on Saturday.