Sorry for long post, I'm crap at condensing
POTA: It has its flaws (acting), but I don't have a problem with the plot. It's a science fiction film about wormholes and time discrepancies, which explains everything imo. A time discrepancy explains why the ape civilisation was there before Wahlberg's character arrives, but was caused by his mission. At the end of the film, we have General Thade scowling in a suspicious, plot hatching manner. If you accept the premise that a wormhole can take you into the future, and another into the past, why not accept that there are multiple ones that take you into different points in time? Wahlberg's character is one of those quintessentially doomed ones, his mission led to the original POTA and then led to changing the history of his own planet.
Apocalypto: Any film attempting to depict the past is probably historically inaccurate in some way or another. Many so-called biopics take many liberties too to make characters more likeable etc. I don't think anyone would argue someone from the tribe depicted in Apocalypto saw the event at the end (but someone from another tribe must have), and it's the significance of it that I find powerful. It's an event of gobsmacking awe, where you watch wondering what has made the film stop dead in its tracks, and then you see an event that changes the course of history and the world forever. And you see the good guy run off and the bad guys stay, and you know their fate will be what they deserve with certainty.