Maybe one of them snores? Maybe they had a fight. Maybe one finds one bed more comfortable than the other...whatever the reason it is not putting you out too much to have to wash one extra set of sheets.
I have the same type of unit available and I figure that if the second bedroom offered them a better night´s sleep for whatever reason, then I am probably going to receive a better review so definitely worth it. With all the problems some guests can bring, I think using the second room, which is technically available, is a very minor issue.