Plot hole: Stuart establishes that there is only one of you and that when you travel through time you can repeat things, but it will be you and not your double that does it. But, at the end, when the Duke is going up the stairs and the uncle says "Where have you been...", the Duke is wearing the same clothes as the first time. Yet we see that he goes directly from the time portal to his house in the ballroom raiment of the later scene. Where did the old clothes come from?
Plot hole: About half way through the movie, the basketball coach is in his office and you can see a dry-erase board behind him, and a couple of dates such as 3-15-99... however earlier in the movie when they are announcing the basketball game they say that it is the 2000 season. They obviously changed the voice over to 2000 after the release date was changed, however the dates on the board are still referring to the scheduled '99 release.
Plot hole: When the police search the white car and the barn they fail to find the compartment in the car behind the boot in which the decoding equipment was hidden. This is completely improbable. It was a standard car, the compartment was not a secret add on, and the police were supposed to undertake a thorough search of everything.
Plot hole: When John retrieves the mail from the postman, Iris dashes outside. Less than 10 seconds after she closes the door, a car is heard, off-camera, honking a horn. Wouldn't John have found Iris so soon after that noise is heard? She doesn't seem to have enough time to allow for a search for her.
Plot hole: How did Dolittle manage to rescue an incredibly heavy bear from drowning? He must be unbelievably strong to be able to drag a bear of that weight. (00:35:25)
Plot hole: The police wanted to take Julian's father away as a Jew because they found out his grandparents (plural) were Jewish. Even assuming they were only talking about one set of grandparents, this would make the father half Jewish, and therefore in the eyes of the Nazis, a Jew. That means that Julian would then be one quarter Jewish, and also considered a Jew. But the police then go on to say that the father is one quarter Jewish, but Julian is only one eighth Jewish, and therefore not a Jew. But he'd have to have only one Jewish great-grandparent to be non-Jewish, and they already confirmed that he had at least two. The numbers don't add up.
Plot hole: Danny receives the telegram from Rafe, telling him that he is alive, at the same time Rafe meets with Evelyn. The telegram must have been sent from Hawaii. Why didn't he just call on the phone? When Rafe reached the U.S. after leaving England why didn't he send a telegram then. In those days it took some time to travel from the Eastern U.S. all the way to Hawaii and there is no way he beat the telegram if it was sent when he returned to the U.S.