When Mr. Magorium asks Henry to name the Fibonacci series from its 11th to 16th integer at 17:15, Henry should name 6 integers, but only names 5. The 5 he names are the 12th to 16th integers of the Fibonacci series. He leaves out the 11th integer - 55.
The length of Natalie Portman's hair changes inconsistently throughout the movie. Dramatic differences can be noted during the hospital scene where in various shots it appears at both it's shortest and longest.
While in the hospital, Molly and Henry are talking in the hallway while Eric is in the background rolling back and forth on his 'wheelie' shoes. Henry begins to walk away from the camera as Molly takes a seat at the front right of the frame, he pauses and beyond him at 47:24 Eric starts to roll from the right side of the hall to the left as Henry starts to turn around. At 47:25 when Eric has rolled about halfway across the hall from right to left, the shot cuts to a narrower shot of only Henry with Eric beyond him where Eric is on the left side of the hall starting to roll to the right side.
When Mr Magorium and Mahoney are dancing in the park and Mahoney rolls out a sheet of bubble wrap we clearly see there is nothing on it. In the next shot of the sheet we can see rocks holding down the corners, which then disappear again.
The goof item below may give away important plot points.
Towards the end of the movie when Mahoney is bringing life back to the toy store, she points at a row of boxes which respond by popping out paper streamers. But at 01:27:17 as the two little girls walk into the shot, the streamers appear in front of them instead of behind as they should be, thereby revealing that the streamers were digitally inserted into the footage improperly.