Hi Godboo, welcome aboard,
If you are not at battlestations, you can go to the crew screen, check the individual fatigue of crewmember and swap in fresh crewmembers. Even on duty crewmen will sleep on the job if they are too fatigued, say over 60-70.
As to why it happens, I have noticed two major reasons:
1) in rough weather, your crew will become more fatigued. In that case you can always dive and spend 6-8 hours submerged and let them rest;
or
2) I notice when you load a saved game, the game assigns a random fatigue factor to each crewman which may be low or high. In that case, all you can do is wait until a few watches have turned over for your crew to catch up on their sleep.
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