Other mistake: In the last episode of season 3, Helen Cutter goes to site 333 to kill off the first hominids. Connor mentions that that's the site where thirteen members of a hominid family all died at once, and no one could ever figure out why. The implication is that it was Helen's actions that killed them off, and we see her doing it. Right after killing them, Helen herself is killed by a velociraptor, which also dies. Danny Quinn leaves their bodies there and walks away. Doesn't that mean that, when site 333 is discovered in the future, they would also find Helen's bones and those of the raptor? I imagine it would cause some confusion if the bones of a modern human and a velociraptor were found in the same strata and the same age as the earliest proto humans.