Plot hole: There are six metal bars mounted around the circumference of the water wheel's axle. In the wheel's interior, when Jack frees himself he lands on his feet, begins to run and promptly hits his head on one of those axle bars, then falls out. Moments later, when Jack returns and runs in the wheel, he is shorter (way more than a foot) than all six spinning axle bars, which would make that previous shot impossible, however humorous it is. (01:52:40 - 01:53:55)
Plot hole: Christopher Columbus speaks Italian while the Huns supposedly speak their native language. Shouldn't Octavius and his Romans speak Latin? (00:34:50)
Plot hole: When the ship has turned on its side for the brief moment, it cuts to inside the ship where a hallway explodes, causing the ship to submerge. The only problem is the people are standing on the ceiling, but if the ship's on its side, they'd be on the wall, not ceiling.
Plot hole: When Magneto lands the bridge between San Francisco and Alcatraz, only the ends of the bridge are on land, with the rest still suspended in the air despite having nothing to keep it there. Magneto could arguably be using his powers to keep it supported, but at the moment he loses his powers it still does not collapse at the center.
Plot hole: At the end of the movie, when the water drains away, there would be no way for a) the amount of water to drain away that did and b) for the mammoths that came through to be completely dry. (01:16:20)
Plot hole: When Farley is preparing to rescue Simon by towing him up with the rope attached to his van, he drops his "cigarette" into his crotch, causing him to floor the gas pedal. His back wheels begin to spin. This is impossible because the vehicle is still in Park. There is even a camera shot of the "PRNDL" proving this. I guess this goof is employed by the filmmaker to increase the dramatic effect of him subsequently slamming the Dodge into drive a second later and careening through the fence. (01:07:35)
Plot hole: When we see the Zenith Team playing softball, it's a scene taken from later in the movie. For one thing, Mr. Pibb is there, even though we don't meet him until the next scene. Second, they're in the room with the UFO, but we don't see that until later. Finally, Zoom's outfit is different than the last scene, but in the next scene he's wearing the same outfit.
Plot hole: Alex and Jack go to Liverpool St. Station to find the guys from Jeff Slater's. This is on the day of the funeral, otherwise it would make no sense going there. But when Mrs Jones sees Alex, she says "shouldn't you be at school?" This makes no sense because Alex would not go to school on the day of the funeral. It's not a character mistake because Mrs. Jones would never make that mistake.
Plot hole: It's one thing to have a small amount of liquid nitrogen (about the size of a standard propane tank, by the looks of it from the Fridge scene), but where did the gallons upon gallons of it during the climactic flood scene come from?
Plot hole: After Jack Frost ceases to be Santa and Scott Calvin becomes Santa by putting on the suit, everything at the North Pole goes back to the way it was. Inexplicably, though, Lucy's parents, who had been frozen by Jack Frost, remain frozen.