Simple idea, but what did they have to eat last night? I once found my Leo with the fur all stuck and dirty one morning, and it was a leechee he brought to his sleeping pouch and slept over... have you tried to gently clean it to see if the stain goes away?
Bacterial infection seems odd to me, as it would imply an infection of the skin or UTI, in which cases her fur would be wet, not just looks so. Could possibly be yeast infection, but I doubt it could appear overnight to such a large area.
Were your Simon not neuteured, I would have assumed that he just went on an agressive overmarking session.
About joey trail, female gliders have been known to have the ability to freeze an embryo's developpment, I recall Pricilla Price exlaining that she once had a female -who was living in an all female colony- give birth to joeys...10 months after have been housed with a male for the last time.