Useless foot missions. I get caught and die all the time, even if I am doing nothing, and it's dam near impossible to get anything on the bases without 10 damn soldiers showing up to light you up. Fix this. Totally unplayable!
Umm.. if you're doing nothing wrong you shouldn't be busted for anything. If you are being busted you are either:
1) In a restricted area
2) Near someone you've killed or a door you have forced open
3) Being observed downloading restricted data
4) You have a bounty on you
5) You have a cloned profile on you
6) You're seen interacting with something you shouldn't be (opening a containment unit for example)
7) You try and do something you shouldn't be doing without disabling settlement alarms
There are bugs with the game, but the stealth gameplay works well and as intended, so there is nothing to fix here.
Once you get practiced its fairly easy to take out NPCs you need to, to get the appropriate authorization, etc. But you do need to learn.
If you can't figure out why you are getting busted, record it happening, post a video, and people can explain where you are going wrong.