I'm not sure I'd go as far as saying it's common, but it's the sort of thing that should get resolved automatically at a marginally run (or better) hotel. If the night audit doesn't catch the double charge, the review of the night audit should find it. While the night audit happens nightly, some hotels may not review them for a day or two. (Friday might not get reviewed until Monday, for example.) So, it might take a few days.
The exception would be a hotel that does a lot of day-use rooms. In a normal hotel, it's easier to spot a double charge because there would be two folios for a single room. But, hotels that do day-use rooms would routinely have multiple folios per room, which makes it a little more difficult to spot these types of errors.
(All of the above commentary is based on experience working at Front Desks as well as my time as a hotel Income Auditor. As Income Auditor, I reviewed the night audit for accuracy.)