If the maroon is a juvenile (and if it's wild caught, you don't know, regardless of the size), then you may have seen normal aggression of the part of the percula. She's the boss and it's HER tank. If the new juvenile does not submit to her vigorously and often, she will beat him up until he does.
You can cross-pair, although doing so with maroons is the hardest since they aren't in the same family as other clowns. That the first fish is a female is a bonus.
Key question: Did the maroon try to fight back? Did at any point did you see them locking jaws head to head? If so, you probably have a female maroon despite her small size. The maroon needs to go back to the store, then.
If the aggression was limited to chasing and fin nipping, and if you saw the maroon submit to her either by laying on his side and twiching/convulsing at her OR by "kissing her" on the cheek (not mouth to mouth), then you are probably okay. Separating them while being visible is a good idea to give him a rest. He does need some fresh water flow, though -- either a breeding net will work or drill a lot of little holes in his container.
Another key question: is your perc trying to attack him in the container?