Plot hole: After the dinosaur kids wrecked the playground, Manny tells Sid, "Whatever they are, take them back" and someone says "What are they?" as well. Later, when Mummy Dinosaur appears, Ellie says, "I thought those guys were extinct!" and one minute later Manny says, "She's a dinosaur!" How could they possibly not see that the kids were dinosaurs if they already knew about dinosaurs in the first place?
Plot hole: The main character never takes the elevator. He only takes the stairs. When leading a workshop he leads a group of people from street level by saying 'follow me' and in the next shot the whole group is on top of a high rise hotel. How did he and the entire group get from street level to the roof together if he never takes the elevator?
Plot hole: Mr. Cranston asks Denise to be the accompanist for the school's production of "Chicago". This is an error. In the year 2009, in which the film is set, this would be impossible since the licensing company which has the theatrical rights for "Chicago" restricts the show from being produced (even by amateur groups and schools) anywhere in the greater New York area while there is an open-ended production running on Broadway.