First of all. If they can trace card access, no employee is going to "borrow" a room to have sex in. I mean, as long as they are using their card. If they aren't using their card, tracing would be pretty useless.
Second of all, I could see the condom getting left that way, but not the standing water or underwear. No one is going to have a quickie on company property and then walk out without their underwear. If fact, if anything, they're going to leave that room cleaner than they found it. If it was a grievance, they could have (and would have) done something more than that. That's just standard guest grossness.
I don't buy the employee quickie idea at all.
What it sounds like to me is a room that was checked out of that day. Maybe a late check out. Housekeeper never got around to making it up. Maybe front desk thought it was made up because there was a software error, or maybe front desk assigned "503" on accident when they meant to assign "305".