Revealing mistake: In the scene where O'Neil is fighting Ra's bodyguard, the bodyguard uses claws and hits O'Neil's back, tearing his shirt and wounding him. But you can see Kurt's "wounds" and torn shirt right before he's hit by the bodyguard (a scene after Ra's bodyguard's claws are shown).
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: After the slave boy gets a cigarette from O'Neill, he reaches out to touch a gun, and O'Neill grabs it and scares the kid away. O'Neill 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.
Factual error: Dr. Jackson states that you need six points in a 3D volume to define a unique position. He then draws six points on the faces of a cube and connects the opposed pairs of points with lines, demonstrating that they all intersect to reveal the unique location. Whether this is really a good way to identify points in space is debatable, but even so, the technique he demonstrated requires only four points, not six. Any two lines that intersect do so at a unique point.
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).
Factual error: The military ranks for everyone but O'Neil are wrong. O'Neil is a Colonel (Full bird), Kawalsky is wearing the insignia of a Lt Colonel, but is referred to by O'Neil simply as Lt., when he should be called Colonel. All the others are wearing enlisted stripes (Ferretti - TSgt, but is credited as Lieutenant Ferretti), the others are also credited as "Lieutenant", but wearing enlisted stripes.