I was on the 'Clear mass transit pike' mission after 3 hours of settlement development (which is how I think the glitch was formed), on route I filled up on loot via killing enemies around the general area of the tunnel entrance, so I fast traveled to Sanctuary to drop it off, when I fast traveled back to MTP new enemies were there, I cleared them again, then fast traveled back and forth only to have the same result. They were tougher enemies each time, ghouls>raiders>super mutants>robots>super human things that wiped me out with Gamma rounds. I was so pissed that I deleted the days save files without investigating further. I haven't played it since so I can't report if the game is working from a older save. A waste of time and a real let down from a game I was enjoying.

In truth I'm glad it's happened now, I've been on tender hooks since the beginning, I knew, as did every beth fan, that glitches would be present, as it happens a big one has happened early in the game, I count myself lucky that I can retire it without wasting hundreds of hours.

I could also see performance issues the more I got into the game, just like Skyrim. The more settlements, companions and jam packed workshops there was the more issues I had, mainly frame rate but also super, SUPER long load times.

Get this glitch fixed, I'm a fan of your concepts but I'm done with Fallout 4. One day you'll get it right on launch!