I've had this happen at least 4 times in the beta to include the latest update tonight with the Advents.  My friend and I will start playing a LAN game only to find out an hour into the game that we're playing different games.  I'm not sure how the heck it's happening as some things are similar, but it is a tell tale when I don't see him expand past his home planet (we're allies) and likewise.  I've played two hours like this before without realizing that we're somehow not playing the same game.  Very weird.