I have a quest to clear out the Kingsport lighthouse. I killed all enemies including turning on VATS to search for nearby mines and disarmed those. However, I can't acquire the workshop because it says clear all enemies. I also noticed in the light house at the top, the yellow bar guard is permanently down now (at one point I had activated it up). Even killed the enemies at the top of the light house. Any idea of what i'm missing?

I would share the link to my YouTube broadcast, but the Forum does not permit URL's. You can try to search on youtube "Kingsport lighthouse glitch"

If you fast travel from there do you get the message 'enemies are near by'?

I am able to fast travel from Kingsport Lighthouse anywhere else.

Maybe one of the enemies got drawn away from the area somehow?

Did you take down the children of atom down on the docks?

This would be my guess. There are usually a couple of them hiding down there, and they seem to not leave the dock.