I have 2 guys being held captive by a Falmer boss. But many times when I enter their area, the Falmer boss and his creature minions are attacking my prisoners from outside their holding cell. The prisoners are set with an AI package to sit on a wounded floor marker and they are set to ignore combat and about everything else. Any suggestions?

Make sure they have no faction that would make it so that they'll become opponents of the Falmer. Add them on a script later, probably after you've engaged dialogue in them, or after you've killed the boss, et cetera.

Nope, no factions either.

Add them temporarily to a new faction as falmer friends?

Exactly. Very aggresive NPCs attack every NPC not being friend or ally.

If I added them to the Falmer faction, wouldn't they then be hostile to me?

Yeah, but I think you can create a new faction that's friendly with the falmer but not allied

They won't attack you because they're still in your faction, but being friends with the falmer means they won't get attacked.