Except Ayla and her tribe are clearly Neolithic people. In short, they were Homo Sapiens Sapiens. Chronopolis' claims regarding human evolution are directly contradictory to the evidence in Chrono Trigger. Having a language at all means that they weren't very far removed from modern humans.
Though, to be fair, the time period (65,000,000 B.C.) put things right around the time that Primates were becoming separate and wide spread as an order. In short, even Australopithecus shouldn't have been around, much less Homo S. Sapiens.
But given that Chronopolis had barely any records on Lavos, it isn't beyond belief that they were simply mistaken about the timeframe of human evolution. With scant fossil evidence, perhaps their estimations were based on tracing genetic deviation (the molecular clock). A simple faulty estimation on the degree to which the Frozen Flame caused mutation in human DNA (as such mutations can be estimated and tracked backwards, offering an estimation as to when species might have diverged) could skew the age of such deviations.
Regardless, relating Evolution in the Chrono series to real world Evolution is a headache.
Curiosity: the Frozen Flame was supposed to influence human evolution... but was it ever established when it got to Earth (and, indeed, if it was even from Earth's Lavos)?