After some ill experiences and our own health and allergies we chose not to accept pets, but as to a fee or damage deposit it may come down to the style of your operation. If your flooring is stone, tile or vinyl and pet pee means a more involved mopping may be time to increase the nominal fee a bit and/or not have these specific folks as guests in the future. If your flooring is carpet and pad and these folks have used your room as a kennel for an untrained pet, then I'd be very annoyed and the only real solution is an expensive replacement of the carpet and pad, and I'd probably be pointing out the damage to the guest and asking for some compensation, yet after the fact, you likely lose.
This sad experience may be a teaching moment, would be for me anyway. I see several choices: 1, no pets, but probably bad for business if you have a following of pet owners, 2, if this is an isolated experience, raise the pet fee slightly to cover such events and consider it the cost of doing business, 3, consider a sizeable up front refundable damage deposit, but that too may deter the nice folks, 4, start thinking about your next room design/upgrade using hard surface flooring.