So this is one is as old as the hills, but here we go:
Beam weapons (laser beam, raygun, plasma wave) will sometimes not deal damage when fired at a player, even though they clearly score a hit. Rayguns have suffered this noticeably for all of NC2, however it only became striking with other beams since 2.2. Curiously, the FPS of the target player seems to effect the likelihood of this occurring - higher frame rates make damage more likely to be shrugged off.