I've just been doing some calculations, and it looks like the lower decks of even a small ship have plenty of opportunity for horribleness. For example, a ship of 25,000 crew can easily produce 2 and a half thousand tonnes of sewage, wastewater, and industrial effluent a day. Given the kind of damage a ship can suffer in combat, imagine the situation is the Main Vats are ruptured. The Great Brown Flood of M41.230 would go down in shipboard history.
And of course, there's the risk of hullghasts, boreworms, maw leechs, etc. What other sort of things can I put down there to make the Explorers feel the need for a long hot shower, afterwards?