Factual error: When the group is travelling through the canyon near the end of the film, they are burning liquor to light the way, yet there is a lot more light than would be given off from this small flame. And none of it is flickering as would happen with a naked flame.
Factual error: The rock samples are from "22 years ago this month," and the solar model predicts a solar eclipse every 22 years. But in order for the sample records to be kept, they must be marked relative to an interplanetary standard. For the orrery to have consistently accurate meaning, it must be set to local years - revolutions of the mystery planet around the sun. One timekeeping is used for records that must be transferrable to other planets and the other for daily use like time of day, but the two cannot be mixed. This makes much more sense than applying the standard cycle to local time - it would totally ignore local events like day, night, and eclipses, all of which are very important.
Answer: The alien did it. Riddick is just starting to change a little bit, but he is pretty upset by her death nonetheless.
Grumpy Scot