This also happened to me. It was when I had two episodes of the same show recorded and the show happened to be on a channel that show adverts and commercial skip was in the wrong place. Luckily the commercial skip flag was only 30 seconds or so from the end of the episode. It was annoying,
Although even more so is when you have commercial skip on auto and the flag comes in the wrong place. Then you have to come out of what you were watching (cause five minutes of your show was skipped for no reason), set commercial skip to skip button then go back to your show and then remember to set it back again.
Royal pain the the ass, the even more annoying fact is that, this only happens on one channel (the one that doesn’t have adverts for revenue in the middle of your show), not sure if this would even be feasible and maybe way to far down the rabbit hole to even consider, although having an option for commercial skipping that ignored certain channels would allow the commercial skipping option to be left on automatic and save interrupting viewing, I told ya.