Hmm, as someone running a B&B this is exactly what I live in fear of. So much so that I have now brought in an automated system to avoid any process weakness, but before then it was something I double and triple checked if I had any doubt. With three different check points I could be fairly sure that if they all tallied then I had failed to take the deposit. The doubt was there once… not nice (although it proved that the checks worked).
So, I would suggest that it can happen all too easily in the trade, but that is probably unintentional and the proprietor will be horrified once they realise. If I had received an email of this type I would react immediately and follow up with a phone call to apologise…profusely. If you use a chargeback request, whilst justified, it will affect their merchant services charges and the punishment may exceed the crime. That said, if you don’t get a reply by tomorrow evening (since weekends can be horrendously busy if they are, for instance, short-staffed due to illness) then I would wholly support the use of that route.