If you destroy/decomission an entire fleet, the ships' maintenance costs are not deducted from your weekly upkeep. (You have to use Details->Destroy to get rid of a whole fleet at once) You get the stated cash back correctly, but the ship maintenance cost stays the same.
It's not a problem if you disband the fleet, then decomission each ship individually. (Even using the same Details->Destory path)
This isn't a huge deal unless you make a habbit of scrapping most of your ships. In which case, it can be pretty crippling.
--LordPixie