The AVP novelization does a good job of fixing many of the plot holes in the movie although I don't remember all of them. I do remember that Sebastian's theory about Antarctica being free of ice several thousand years ago is explained in detail. There are similar theories in real life which claim that the Egyptian pyramids were actually built about 12000 years ago. Sebastian never says "what are those" when looking at whale bones in a whaling station and the way to open the sarcophagus has nothing to do with the date but has something to do with the constellation Orion.
However, the novel introduces one really big plot hole that wasn't in the movie, which completely ruins it. In the movie, when the Queen calls, 6 aliens come to set her free. In the novel hundreds of aliens come, with no explanation of where they came from. I don't know how this ever got published without anyone noticing. Maybe it was this way in the original script.