I has been a while since I watched the movie, but as I recall it was very inaccurate. Aside from the fact that the movie has absolutely no idea when it is supposed to be set, it has numerous other mistakes. The first problem is with the village itself. The houses far more closely resemble buildings from Amazonian groups than from the Maya. Second, we don't see any farms/crops, implying that these Maya are tribal hunter-gatherers. This is fundamentally wrong. The Maya were an urban/agricultural people, and farming maize was an essential part of their religion. Almost all their philosophy, world-view, and relationship with supernatural powers was (and still is) framed around cultivation.

The raid on the village is not inaccurate in and of itself. Both the Classic and the Postclassic had periods of intense raiding. However, there are political elements missing. Each village would be linked to a network of settlements that fell under the control of a city-state (called and altepetl in Central Mexico), ruled by a petty king, to whom the village paid taxes. In theory this city-state also protected its citizens from such raids, and so should retaliate. They may not, depending on what else they are doing. The problem here is that the village is portrayed as completely isolated, which strains credulity. The Maya world was crisscrossed with roads that connected cities to their neighbours. Even villagers should at least take their harvests to market or leave their town to visit important ceremonial sites.

Then we get to the city, where we find several problems. The prisoners are stunned and awed, apparently never having seen a city despite this one only being a few days away. This is ridiculous. The Maya world was covered in cities. There were so many that almost every rural community was within 10 km (or was it miles) of a temple. The villagers should not have been shocked. They would have travelled to similar temples for their own rituals. Another big problem is Kukulkan worship and heart sacrifice. If the story was set in the Postclassic this would be fine. However, so far the movie appears to be set in the late Classic, when heart sacrifice is rare and Kukulkan absent. This is an example of the time confusion the film has.

The arrival of the Spanish throws the film into a vast amount of time confusion. A lot of the dress, jewellery, and architecture would be acceptable for the Classic. However, they are about six hundred years out of date by the time that the Spanish arrived. This is most notable with the architecture. Postclassic Maya cities in Belize and Yucatan used Puuc architecture, which is quite different from Classic era building styles, yet is nowhere to be seen. The decay of Maya culture, as seen in the film, may be appropriate for many Classic period sites, but is completely inappropriate for the Postclassic when Maya society had stabilised.

I'm afraid I cannot go into more detail as I have not seen the movie in a very long time, and I'm sure I've missed some important details. However, you might want to check out the History Buffs on Youtube. They did a video on Apocalypto and deconstructed it quite thoroughly. They will give you a better overview than I have done.