No attack going on. I just noticed on my pipboy it's not showing the correct number of settlers in Santuary. So I go back there, things look ok... But suddenly my crops start disappearing right in front of me. Then it destroys my generators and water. I look in my Aid section and all my food is gone. Literally over a thousand items vanished. I go back and check all my saves for the past 6 hours and this happens every single freaking time I load them. This game has more game breaking bugs than any game I have ever played on a console... in 30 years.

Since I can't post links, copy this code to see my video and skip to 1:21. Corn just starts falling down, generators that were fine when I got there suddenly are smoking and broken, pumps destroyed. Everything is nuked and there is no battle,non intrusion... Nothing. Here is the YouTube search code: I_ce6iZvXM4

Happened to me too. Had to repair the generators and water pumps and the plants. Needless to say I was highly irritated.

That does look like a glitch of some sort to me but I know there are supposed to be enemies capable of using stealth technology but I don't know if that's happening to you or not.

I noticed you have damaged stuff like generators, crops, and probably the water pumps, and I guess since they're damaged they are not working since they only produce when fully repaired, so no power, no pumps, no water, crops die, villagers eat food in storage.

(spoiler) Also there is this: http://www.gamefaqs.com/boards/164594-fallout-4/72844668