While I can't speak to accounting practices in foreign countries, I did work in hotel accounting here in the United States. Where I worked, there are layers of checks to ensure everything is proper.

In the set-up I worked under, the Front Desk only handles in-house guests and those that have checked out that day. Once the night audit is run, the Front Desk no longer has control over the folio for a guest's stay. As such, I think the notion that the Front Desk was "messy" with your account is unlikely.

Where I worked, I was the Income Auditor. In that position, I audited the Night Auditor. (Of course, the Night Auditor is the person who audits the Front Desk.) Essentially, I was the third layer of checks to ensure guests were correctly charged. My work was signed off on by the Hotel Comptroller, who was the final layer of checks.

As Income Auditor, I was a Monday-Friday employee. On Monday (or Tuesday after a holiday weekend), I'd go through all the audits from the weekend. If I caught anything, I'd make the appropriate charge/credit to a guest's credit card. In most cases, I wasn't required to contact the guest to alert them of the charge/credit because it usually wasn't a huge charge.

I'm speculating, but I'd guess that something was caught during one of the various accounting checks that happen. The only way to know exactly what happened will be by contacting the hotel and asking.