Anyone offering their private residence as a temporary lodging (minpaku) must follow laws covering ventilation, dehumidification and damp-proofing, cleanliness, etc. Check the booking site again for the details regarding the cleaning fee-whether it is required or not and how to pay it. If nothing is written about payment of a cleaning fee, or the information is displayed in such a way that it is very hard to find, you can tell the lodging owner and site staff that you cannot understand why you are being charged, and talk it out.
However, if the guest has caused a problem during the stay, the responsibility is on the guest.