These games happen when the host of the game kicks a player from the original 4 that was matched. Its stupid allowing the kick function in pantheon and skirmish games, as there is no replacement logic in place, so the 3 remaining players are always doomed to play an uneven game if any kicking takes place at all.
Another case where this might happen is if one of the 4 inital players think the game is taking too long to start (someone not connected yet) and presses the cancel button, he will drop out and the remaining 3 are doomed again.
The only solution to this right now is to be very observant and quick, if you notice one of the 4 players suddenly dissapear from the connection window, quickly hit the cancel button and drop out! Sometimes the game starts so fast after one person leaving so this is impossible though.
Thats just how the flawed logic works right now. Very beta-ish, unfortunately.