I had this when first starting out on the game.
What it ended up being, is that my transit TC was too high, and I'd be taking damage as the game reverted to 1x TC, too late for the crew to 'spot' an a/c.
Then someone mentioned that a TC equal/less than 256 was the best for spotting a/c. I've since then always run at a max TC = 128 and never had an aircraft sneak up on me.
I also use a lower fatigue model... maybe the watch are dozing.