this happened with the advent too. explanation?
My best guess would be that you're looking at the illuminator vessel, which has two beam weapons on its sides in addition to a primary beam weapon up front. Hence, each illuminator fires three beams at a time and they will usually strike different targets.
There was a bug last version that caused the illuminator's beam weapons to deal additional damage, but if you're fully patched this should not be an issue (the illuminator is a mediocre unit currently)