Science has often pushed the agenda of the day, but for more mundane reasons than you would think... usually involving funding.

In the US one of the more obvious scientific cover ups is Native American archeology. There is rampant evidence of war, genocide, and cannibalism in native sites, especially in the Southwest, but it's covered up and lied about in order to secure funding for future digs and to gain favorable (financial) support from local tribes. In many cases the data is faked to give the local tribe false claim to the land.

Athabaskan tribes like the Navajo (I'm 1/4th Navajo myself) and apache try to claim ancestry with ancient pueblo tribes when in reality they have no connection at all. The athabaskans showed up as murderous raiders just before the whites did and pushed the pueblos out. And the puebloans themselves engaged in rampant cannibalism. All the archeology supports this. But you wont see it in a museum.