Are you sure they aren't using another type of weapon as a secondary attack, like mass drivers or missiles?  Pardon me if you already know this, but unfortunately shields in GC2 aren't traditional sci-fi force fields, they only protect you against beam attacks.

I've also taken some damage on ships that should be immune to the weapon type they were getting hit with.  Not a lot, but it does happen.

If memory serves me about combat, the attack and defense values are the max you can do.  The damage you do/can withstand that round is randomly determined from 0-100% (MIN increasable from the Luck ability).

You must have rolled low a few times and him high...