Hmm...I think it may be a bug caused by starting the mode incorrectly. We started out playing Coop Mode. Four players were added and Player 1 played their ball. The start button was then held, which switched it to Team Vs Mode (I wasn't expecting that to happen). From then on the reactors seemed to progress as if in Coop Mode, meaning that as reactors were destroyed they were destroyed for both teams. However, as previously noted if a reactor was critical no shots were illuminated for destruction for the other team. The scores were still keeping track as 1 and 3 vs 2 and 4.
PS: On a side note. I wouldn't mind seeing Team Vs Mode to accept 1 and 3 vs 2 alone. I have a number of non-pinhead friends and that might create a fun handicap mode.