Nothing worse than having to take a dump on a boat. I get up crazy early on dive days to "get things moving" to avoid this exact issue. I find it literally one of the worst things ever! Thankfully it's only happened to me once or twice on charters with really long rides out (Channel Islands in CA and wrecks off Morehead City NC). Those were very large boats though and it was manageable.
On a related experience, on the Olympus boats in Morehead City NC, a boat rule covered in the briefing is NO USING THE TOILET WITH DIVERS IN THE WATER!! Their toilets discharge overboard, at least they used to. Well, my buddy and I were on the mooring like doing our safety stop and noticed chunks of brownish flotsam floating by. Yup, you guessed it. Some bonehead had ignored the briefing and that sacrosanct boat rule. Did a super thorough gear rinse and shower after that charter!!!!