As the title suggests, I am wondering what determines the levels. I thought it was the enemies but I have only Romulans which all say level 16 is required so is there another factor I am not aware of? My mission currently says Level 41+ which is much higher than I designed it for
As far as I know enemies is the only determining factor. Is it possible you have a higher-level group somewhere. Even if they are skinned as romulans, they would still raise the level. Also make sure you haven't accidentally left any mobs around that you aren't using. Say you put down a borg mob earlier then decided not to use and it, but didn't delete it.
One other thought, and this may not actually be a cause, but where is the door to your mission? It could be that if you put the door in a high-level area, the game adjusts the mission level to that area. I've never tested that, it just occurred to me now.