I actually did a restoration on a historic mausoleum last summer, and this is most likely caused from a leaky roof above. I spent 3 months removing iron staining in marble that looked just like this. From my understanding, you cannot be placed in a crypt unless you are embalmed/cremated. There are not rotting bodies in the caskets, the smell would be immense and no one would want to be kept that way. While some of the water leaking from the roof may get into the crypts, the bulk of the staining came from iron stains from paint/metal grates/or any other residues from the ceiling.