Aliens (from what I understood of the plot) deeply wanted the 13th Crystal Skull returned back to their circle of skeletons, so they could re-animate, meld/merge, and get the hell out of
Dodge this planet.
This is clear because they told Indiana Jones (and presumably, Oxley before him) to return the skull.
Yet, they also caused a warlike, hostile tribe of natives, to be preventing anyone who would return the skull, from getting it into the pyramid - first, Oxley couldn't get by them and had to return the skull to the original place (this is important, because Oxley had the skull with him the first time around, and couldn't get by them). Then, Indiana Jones and Transformer Jr. barely escaped with their lives even AFTER showing the natives the skull (which was presumably how they were supposed to tell friend from foe - but didn't help Oxley at all).