If a chracter is fighting more than one enemy and one of them has an effect that happens during the battle such as rolling two dice or fighting only characters of certain alighment, does it still apply for both enemies?

They fight as one, so yes. The FAQ gives a good example with Cave Troll + Goblin fighting as one. It the Cave Troll ability to regenerate makes the combat a stand-off, the entire attack is a stand-off and the Goblin survives as well.

I don't know which Enemy are you referring to that "fights only characters of a certain alignment. If it's the Ivory/Ebony Sentinel, they can be evaded by characters with a certain alignment; since evading happens before combat begins, that effect is applied only to the single Enemy, not to the group.