- Continuity: 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. Eric wheels to the right side of the hall, then there is a close-up shot of Henry. Eric is back on the left side of the hall.
- Errors made by characters (possibly deliberate errors by the filmmakers): When Mr. Magorium asks Henry to name the Fibonacci series from its 11th to 16th integer, Henry should name 6 integers, but only names 5. The 5 he names are the 11th to 15th integers of the Fibonacci series. He leaves out the 16th integer - 987.
- Continuity: 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.
- Continuity: In the hospital, while Mr. Magorium is standing and speaking in the hallway, you see the boy walk into the shot and then run out to the right. In the next shot you see him back in the hallway where he had just been.
- Errors made by characters (possibly deliberate errors by the filmmakers): Magorium states that "It takes Shakespeare, a genius, to come up with "He dies." The phrase "He dies" appears in the stage directions, not the text itself. In fact, William Shakespeare never wrote any stage directions, so he did not write "He dies." This, along with all the other stage directions in Shakespeare, was added by later editors.
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Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Revealing mistakes: SPOILER: 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 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.
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