Continuity mistake: The pen used in the beginning of the drawing is different from the solid blue one used in the close up shot. Also, when the camera goes back to a wide shot, the color of the drawing on the whiteboard changes from blue to black. (00:17:40 - 00:18:35)
Continuity mistake: When Jackson is in the meeting about the symbols, he circles the seventh symbol with a blue marker. In the next shot, look close and you can see that the blue circle around the symbol is gone. (00:18:20)
Continuity mistake: After the slave boy gets a cigarette from O'Neil, he reaches out to touch a gun, and O'Neil grabs it and scares the kid away. O'Neil is then holding the gun with the barrel pointing towards the door, but as the angle changes he is suddenly holding it at a different angle, pointing down to his right and away from the door. (01:05:30)
Continuity mistake: There is no necklace on Catherine's neck when she greets Jackson in the room with the cover stones (00:13:39). After they have shaken their hands, the necklace appears on her neck suddenly. Then it disappears again. Also, after Catherine has given the necklace to Jackson for bringing him luck before his departure, the necklace appears on her neck again when she is in the control room during their departure.
Continuity mistake: When the men are in the pit of water the man who says "Colonel it's us", his dog-tags change from on his chest to back several times between shots.
Continuity mistake: The bomb's countdown starts faster than a second between numbers change, then eventually gets to about 1 second/change, then goes faster, etc. Its speed keeps changing from shot to shot. Also, the numbers are inconsistent and don't match the time passed between shots of the same scene (i.e. one second later, the countdown can be 5 numbers down).
Continuity mistake: RA continues to wear the necklace at the end of the movie when it was taken from him by Daniel before he left the spaceship via the transporter.