There were 6 people facehugged in the Sacrificial Chamber, then 3 more (not counting Sebastian) were captured by warriors later on. So there should be a total of 9 aliens. Scar kills one, Lex kills another and then Scar hits 2-4 aliens with his plasma cannon. Then we see exactly 6 aliens rescuing the queen. Presumably there were no more left in the pyramid. So there were 10-12 alien warriors depending on how many Scar shot. Either a few of the facehuggers laid two embryos inside their hosts or the Predators somehow missed several aliens in the 1904 hunt and they've been hibernating for 100 years! Once the hunt was over the pyramid would've stopped shifting and the surviving aliens would've been trapped. I know this theory requires the Predators to be careless but they were careless to allow an alien to get to the surface in 1904 and they were careless not to check Scar's body for alien infestation.