@Stefanie5 I have an entire home listing too and I'm always concerned about extra guests being snuck into the place without my knowledge or consent. I believe it only happened once: the extra pillows / blankets removed from the closet were the tip off.
Unless you are onsite to monitor the guests, you are open to this kind of behaviour.
What I do is ask all guests to read and agree to my House Rules where I state the maximum number of guests (in your case you would mention the extra guest charge) before I accept their reservation. Obviously I don't use Instant Book. I also confirm that they are not bringing children and pets. In your case you could also ask for the names / ages of the guests and inform the booking guest that anyone else entering the property will be asked to find accommodations elsewhere.
As for the mess they left, the guest who made the reservation is the responsible person and your review should reflect that. If you can't prove there were extra people there, I wouldn't mention it. The kiss of death on a review is "This guest would be better suited to a hotel".
Hope this doesn't happen to you again!