As far as raider or supermutant infiltration, I don't really see it as that big a deal. I use plain ol'wire fincing that I can just jump over coming and going, so I'm not surprised when badies get inside my perimeter. The thing is that if a supermutant appears inside the compound, I figure he used a stealth boy to sneak in, If raiders appear, they just must have jumped the fence.
Being a chess player, I also know that defense doesn't win, so I set my defensive turrets back to back in a tripod setup. My building is large, my compound is small, so it's not hard to cover. If my settlers want to go outside the wall, it's on their heads, eh?
If my crops die, I figure there is a reason. I've tried planting a garden in RL, and I have a black thumb from hell. If I plant it, it dies. Thus, I don't question dead carrots and melons overly much.
The things that DO bother me, are events that I can't really explain away in a logical fashion. I find writing stuff off to gremlin activity is a bit immersion breaking. So, when I come back to my stronghold settlement and find all the light bulbs missing and the place dark it bothers me a little. The thing is, they don't just stop working, they are actually GONE, fixture and all. Then I go to replace them, open my workbench menu, and magically all the lights are back in place and burning brightly.
that's when I think my character's spending too much time talking to Mama Murphy...