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: Nick's necklace is a string looped through a ring, but sometimes the string makes only one pass through the ring and sometimes two.
Continuity mistake: Right after Aki saves Gray and turns around to pick up the canister containing the plant off a table there is no table or ledge. If you watch the movie with the commentary one of the members involved with the movie says that it is floating on nothing. (00:16:50)
Continuity mistake: In Session 24, Faye gets into her aircraft and Ed all of a sudden looks down at Faye, from on top of the roof, and starts talking to her. Look at the back of Ed's shirt, it falls up and goes past her neck and rests at her head, when the camera cuts to a front view, the shirt is above the shoulder line. (00:14:20)
Continuity mistake: In the shot of everyone chanting, "disco ball!" Hermey is seen in the background, but two shots later, Hermey has disappeared. (00:19:00)
Continuity mistake: The arc-shaped garden plant directed the protagonist to someone who can help him. A nasty human armed with shears walks by and starts his torture; he kneels by the plant, in a zone with no shadows, and in the next shot the whole section of ground is in the shade. (00:39:40)