They look like craters to me. The trick appears to be to look at all those smaller craters rather than just concentrate on the larger ones.
I'm assuming the lunar astronauts didn't get confused very often, because a vast majority of what they were looking at would have been craters - so regardless they would have been expecting them (plus, being in a moving spacecraft might invoke a bit of parallax to help them out).
I reckon they're craters - based on the angles of the "black out spots" - if you look at the "craters" angle they make sense, but do not when viewed from the domes perspective.