I had no trouble with the episode "Bones of Contention." But that is because I actually have some familiarity with archaeology and the Kennewick man controversy (on which this episode was based).
They never properly explained the controversy that the skull being classified as "caucasian" caused. It doesn't effect Native American land rights, but rather causes issues with the Native American Graves Protection and Repatriation Act or NAGPRA (which basically says that all native remains and grave goods found on public land must be returned to the tribe they originated from). Granted, NAGPRA isn't the most exciting topic in the universe, but without explaining it the controversy seems to be over Native American land rights, thus getting people up in arms over nothing.
However, I did enjoy the episode (if not the fan reaction to it), and I thought that the team interaction was very good. And there were quite a few good lines ("Someone needs to circulate that memo.").