So I had to go to the National Guard Recruitment place to find the fallen BoS members and I naturally cleared it out. Now, on the quest, Ghoul Problem at Greentop Nursery, I'm required to head to back to the National Guard Recruitment Office and clear out all the ghouls...which are already dead. And it won't let me complete the quest. Any ideas?

yup gonna get that a lot don't worry though it's not as difficult as the first run through and a lot of the stuff restocks itself it's a great way to get mats for crafting & some exp I think I have cleared the super duper mart a dozen or so times so far lol

Lol but my issue is that there's no more ghouls at the National Guard Recruitment building because I killed them already

They will re spawn after a certain amount of in game time. Don't worry. Just do something else for a while