Continuity mistake: In the beginning scenes, where Milo Thatch is practising his proposal, he slides over (face forward, chest against the board) a chalk drawing of a map detailing the location of Atlantis. When he realises he wiped off the drawing, and sees it on his clothes, he stands in front of the blank part of the chalkboard, "filling in" the space with the map that rubbed off on his shirt - the only problem is, that the image should have rubbed off backwards as he was facing the board when it transferred to his clothes. He could not simply stand in the place of the missing map face forward and have it read properly.
Continuity mistake: In some scenes the adult Atlantean princess has some of her hair tied up at the back but the next minute it is all down.
Continuity mistake: When Milo is emoting to Sweet about how he is the reason that Rourke got the crystal, he goes to and sits on a red barrel shaped thing. When he first sits down, his bag is slung over his left shoulder (HIS left not OUR left), but in the next shot, it is slung over his right. (01:09:50)
Continuity mistake: When Milo is practicing the lines for his speech, a shield is leaning against a wooden pedestal. There are quite a few differences in the shield between when it is first seen and when Milo picks it up about a minute later. It's much smaller and flatter, the colors are darker, and the grey ring around it is wider.
Continuity mistake: When Milo wipes the chalk off of the board onto his vest, he is shown with his vest completely closed. Just after that his vest is completely open and then closed again in the immediate next scene.
Continuity mistake: When Milo and Kida are trying to figure out how to power to the vehicle using Kida's crystal, the crystal is removed from around her neck to power the vehicle. However, in the next shot the crystal is back around her neck, still powering the vehicle. Then in the next shot the crystal is missing again, but replaced in the next shot, once again.