Plot hole: When Lara and Reiss (and later Terry) enter the cradle, Pandora's Box is floating on top of the black acid. After Lara kills Terry and returns the box to the acid, the box promptly sinks. Obviously, due to the lethal nature of the acid, the writers needed the box floating on top but there is no "story-line" reason as to why it would sink when returned to where it previously was.
Plot hole: When we first see Lara in her wetsuit, she has a back pack attached to her harness, a torch on her left shoulder, some sort of pistol-thing on her thigh, her 5-barrel dart gun by her left buttock and a little pouch in the small of her back. In the temple she takes off the pistol-thing, dart gun and backpack, yet after climbing the statue manages to produce a video camera, safety spectacles and a cutting/welding device from somewhere.
Plot hole: When Lara and Kosa are leading the 20 natives in search of Pandora's box, Lara suddenly slows down and says, "We're getting closer." One of the natives (the one who said he'd stay with them to the end) says something to Kosa. Kosa says to Lara, "He wants to know how you knew (that they were getting closer)." Since Kosa had been translating in both directions, how did the native know that Lara said "We're getting closer"? An earlier response to this indicated that maybe the native "knew a few words of English". If you think about it, that's impossible seeing as how this would have been his first contact with the language. From the moment that Lara arrives in the native village, Kosa translates in both directions for everybody.