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.
Other mistake: When Milo is practising his speech, he jumps over the blackboard to answer the phone. The top of the blackboard rests on the desk, but when he slides back over, it swings all the way round . If it hit the desk one way, it would have hit the desk swinging the other way round.
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.
Plot hole: There is no way that 'coast of Iceland' could ever have been mistranslated as 'coast of Ireland'. For this to have happened, they would have had to have thought that the 'C' rune was an 'R' rune, but they had already deciphered the word 'coast', so they knew what the 'C' rune was. The 'O's are the same rune and the 'A's are the same rune, plus there is one rune for every letter, so it it's a direct letter-by-letter translation.
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.
Factual error: Milo says Audrey is a "teenager". Which she is, but this is 1914! People didn't use that word back then. He probably should have said "adolescent" or something.
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.
Factual error: When Milo returns from his underwater investigation with Kida to find his companions armed, we see Mole holding an old-style submachine gun similar to the Russian PPSh-41. But it's 1914, and the first submachine gun - the German Bergmann - wasn't invented or to be introduced - until 1918.
Factual error: When Mole shows off his dirt collection under his pillow, each dirt pile has a flag sticking out. However, several are either incorrectly drawn or could not have been in use in 1914, the year in which the film is set. 1: The Welsh dragon flag was not officially adopted until 1959, and since Wales would not begin devolution in earnest until after the Second World War, it should not even be a separate entry. 2: The Nepalese flag used is the post-1962 version with differently-sized triangles - the flag in 1914 would have had triangles identically sized. 3: The Turkish flag used has a crescent that points diagonally towards the upper right, whilst the flags used by the Ottomans in 1914 had crescents which faced the right. 4: The yellow lozenge on the Brazilian flag should touch the centres of each edge, but is shrunk in the film's version. 5: When zoomed in, the flag of Poland can be seen. Poland did not even exist as a country in 1914, and would not be reconstituted until 1918. More distressingly, Mole seems to be missing several samples from countries neighbouring those seen which he is likely to have travelled through. For example, to get to Poland he would have had to have gone through Germany, Russia, or Austria-Hungary, between which Poland was split. To get to Wales he would have had to have gone through England. To get to Nepal he would have had to have gone through either China or the British Raj. Disturbingly, he has no French dirt in spite of being a Frenchman.