The "Xibalba Nebula" in the movie is the Orion Nebula - which is not gold and does not contain dying stars, unlike in the movie. It is largely pink (from ionized hydrogen gas) and is a stellar nursery where young stars are forming. The first stars to die there will be massive and will not create nebulae first (they will supernova instead).
The map used by the conquistadors to find the Tree of Life is erroneous. The priest says the three points which form an equilateral triangle on the map are Chichen Itza, Yaxchilan, and Tikal. However in reality, the three Mayan sites form an obtuse triangle, with Chichen Itza being the northern-most and the eastern-most point.
The seed Tommy is planting at the end is from a Liquidambar styraciflua, and should not be green during the heart of winter. Additionally, a L. styraciflua seed of this maturation is most likely immature and will not germinate, regardless of the season.
Tikal is mentioned by the queen's priest, however, it wasn't discovered until the mid 19th century, and the name Tikal ("place of voices") was applied only in the early 20th century by archaeologists. This scene is a novel-within-the-film written by Izzi Creo, whose research may not be perfect.
The goof item below may give away important plot points.
In the final scene, Tommy plants a tree seed pod at the foot of Izzi's grave. The seed pod is from a Sweetgum tree but the pod appears to have lost its seeds already. The sweetgum seed is actually smaller than a grain of sand. It is disbursed by wind and rain from this pod. The pod never generates a tree directly from it.