Are there any televisions in your settlement? There seems to be an issue with electrical items (radio, tv etc). Remove televisions - turn radios off before leaving the settlement. Do not fast travel from within the boundary of your settlement. If possible store your recruitment beacon before leaving the settlement (still has a signal when turned off).
Also check availability of the beds for settlers - seems to be an issue with AI pathing to beds for each settler - if possible manually assign beds to each settler and check they can get into the beds as well.
The pip boy functionality in regards to your settlements is buggy as well. As an example - pip boy showed sanctuary had no beds and no defence - when I arrived back there (no fast travel at all in game) the settlement was back to normal.
All we can do is hope Bethesda fixes the issues in regards to settlements (I didn't have a single issue in my first play through but have with every other single play through since. I don't know if it is a 'trigger' for these bugs but it only happened since I did the last patch 'update' (I'm on Xbox One).
It's really annoying as I've had no other issues with the game and it has run smoothly with no problems at all except the settlement issues. To think they played this aspect of the game up during their E3 showcase and it turns out to be one of the most buggy parts of the game - go figure!
If you look online there are a lot of posts/articles/videos in regards to the settlement issues/bugs/glitches.
I hope this has helped in some way