I don't remember this happening in skirmish games, but I've had something similar happen in some board games. It's pretty unpleasant.
I'm always concerned that the losing side still has a chance to fight until the end of the game. It's one of the reasons behind some of the Karma mechanics.
I'm making notes for the new version of the game. Among them, I think about making Karma more useful for the player depending on the number of their models out of play. It still needs to be tested, but I hope it helps with the balance.
I feel like there's a fine line between giving the losing player a chance to continue and "punishing" the winning player. It seems quite easy to get the dose wrong.