Audio problem: When Bond and XXX are following Jaws in the ruins, we hear his footsteps when he walks but not theirs when they run on the same concrete floor. (00:40:55)
Audio problem: After Jaws rips open the roof of the van, Anya says, "The key!" when she snatches the keys out of Bond's hand, but her lips don't move.
Audio problem: After Bond sets the timer on the bomb at the end, the ticks don't add up. There's a definite tick each second, and you can count 12 of them after he starts it, then we cut back to the bomb and only 7 seconds have passed. (As a vague trivia aside, coincidence though it is, on the UK DVD he pulls the pin out at the DVD second timer ticks onto "07").
Audio problem: When Bond knocks the gun out of Shandor's hand during the fight on the roof, the sound is definitely not a gun on a stone floor - and it comes too soon after the gun leaves his hand. It would not have reached the floor yet.
Answer: First, it was indeed filmed at Karnak. Second, he rescues her because they are, for the time being, on the same side-therefore, she is an ally, and Bond won't just leave her to drown/die. I think, if he is even mindful of her promise during the heat of the moment, he would still consider it wrong to leave her behind; while the mission is on, she's a colleague in distress, and that's that. Once the mission is over, she can do what she likes, and Bond will deal with it then. (Though his surprise when she first draws the gun on him in the escape pod suggests he wasn't taking her threat seriously, so...bit of a freebie for him).