For some perspective, in my years of actually working in the industry, with probably thousands of check-ins, it's only happened a handful of times. And if I subtract out the times it was caused by that "pending" state I mentioned earlier - which always caused the second guest to arrive right after the first anyway - I can think of maybe 2 or 3 times.
If you stay at well-managed properties with strong processes, it really should never happen.
FYI - standard compensation started at a sincere apology from a manager, comped breakfast, and an upgrade if possible. Most managers I know take it very seriously. (But then again, most managers I know are skilled at managing their properties, so it isn't a frequent problem.)