As far as I know, that only happens when you dock at a base which is not your own. You may also notice that you also cannot modify your submarine. If you sail back to your home base (where you started, or were transferred to), you should be able to give your crew the medals and etc. they earned.
You can always just sail 25km away from that port and "teleport" to your home base if you don't want to go the whole way back.
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