i noticed a couple of times the super mutant nest near rivet city was missing the nasties.
That's not uncommon. There's lots of spawn points where the first time you go through certain creatures don't appear, but the next time through they will be. Creature spawning isn't necessarily a fixed thing in this game, there's always some variations, which make things a bit more interesting IMO. If you really want those ones to appear, just save your game then reload, they'll probably be there then.