The thing is with Rub 1.43 crew never "recover" when you put them in "rest-areas". They will only stop being more fatigued. This mod is trying to simulate combat stress and this will be better and better after just a few patrols.
You have to be careful how you use yor men and only use them when they are needed. All other situations they should be in "resting compartements"
My experience is that this mod can feel strange in the beginning, but after a while it works nice and crew management is not so needed anylonger. Important is to get qualifications to your officers and petty officers. That's a good medicine!
I think there is about 100+ posts in this forum discussing + and - about this feature. Try the search function and look whats written if you want to learn more about it.
I also recommend the "Read me" file in Rub 1.43.
Good luck
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