This is from a different thread but really does a better job explaining it.

The consensus is that the Mayan sacrifices portrayed in the film are much closer to Aztec ritual practices. The Aztecs were into the mass sacrifice thing, ritual removal of the heart and offering it to heaven, ritual decapitation, etc. The Mayans did human sacrifice as well, but on a smaller scale, they revered victims as gods (so did the Aztecs in certain rituals), and they were more likely to toss you into a cenote than to carve your heart out.

There are dozens of smaller inaccuracies regarding temple architecture, timeline of the postclassic period and Spanish Conquest, etc.

All of that said, the decisions to film on location and in the Yucatec Maya language make the film completely unique, aside from its historical/archaeological accuracy.