I submitted a bug on this a while back(with dump, etc) but my buddy and I have tracked down that this particular problem is definitely tied to having one player in a sub screen when the other player ends his turn. It then sometimes doesn't successfully transfer the turn.
We have initiated a protocol where we dont go in a subscreen(govern,tech,planet management, etc) while its the other guy's turn without telling them(and they then wait to end turn)
With this protocol we are able to play much longer without issues.
tom