This isn't really an issue with NMM as you didn't use NMM to put them in the wrong place. Any files that aren't in that list then get auto sorted to the best guess location and that usually solves it for me. If it did happen that it somehow got glitched up like that, I keep older load order lists to be imported for quick resetting to a previous state.
If this ever happens to me (did once, was a broken mod from the author), I go through the whole order just checking which files require what masters and make sure they're not screwed up in the wrong order. RE 1: This usually happens (that I've encountered) when somehow a master got placed after a plugin that required it, or if 2 files somehow were saying they both need each other as a master. Issue 2) NMM locks up for some time when you change the load order through Vortex. Issue 1) You can't manually change the load order inside NMM.
Neither issue appears to be a bug in NMM, which I'll explain below.
