I honestly can't say I remember the movie all that well, but he was going after the crystal skulls, which have been found around the world. I know there is obvious debate/belief that they are fakes, but he was still going after artifacts. So, sure, aliens might be out of his scope on paper. But the crystal skulls are in his wheelhouse and if they lead to aliens, that's his game. Just like the supernatural isn't what archaeologists investigate. But when they popped the lid off the Ark, and ghosts flew around killing Nazis, everyone was fine with that.