This is probably due to a longstanding bug that never got fixed. Alt-tabbing, and probably certain programs that use popup messages (like an annoying attention whore antivirus program) can cause the game to lose track of your submerged surfaced state. This has a couple of effects.
The most commonly noticed is "The CO2 bug" where surfacing does not clear the boats CO2 level.
Sometimes you can see your crew out on deck through the periscope or on externals when you are submerged.
I have also observed a link with spotting as well. I have seen enemy ships detect me when I'm submerged at 400 feet, silent running, moving at 1 knot, and several thousand yards away. I have also seen my deck watch crew be unable to spot targets that it should easily be able to see when the CO2 level isn't cleared.
The fix is to simply save and reload.
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