I haven't seen or heard of it happening, but my guess is that the IRS would only invoke that provision to deny an otherwise-EPRCS-sanctioned self-correction in rather extreme cases.
Two categories come to mind: (1) intentional schemes by people who are obviously trying to game the tax code with plans that clearly violate at least the spirit of the law; or perhaps the overall plan is in good faith, but the taxpayer appears to have intentionally committed the specific error in question and was counting on the validity of the EPCRS-sanctioned self-correction to further an abusive tax scheme (the IRS deals with people like this all the time; I would be shocked if there aren't examples in this category where the IRS has thrown the book at the taxpayer, so to speak), and (2) plans that may not have intentional compliance failures, but where fundamental negligence is apparent (e.g., a plan that is being operated without a plan document, a plan whose assets are being intermingled with employer assets or being used as a piggy bank/source of loans by the CEO; plans (especially large or midsize plans) that lack a fiduciary committee, where the board is nominally the fiduciary, but in reality it is being run on a day-to-day basis by people who do not have any formal grant of fiduciary duty, who are not operating the plan consistently, and who are not regularly identifying and correcting plan errors).
I doubt the IRS will invoke that provision in the case of a plan that is appears to be operated in good faith, with a fiduciary committee that meets regularly and addresses a variety of potential compliance questions at each meeting, that generates substantive minutes and has periodic discussions with ERISA counsel that routinely result in self-corrections when errors are identified.
As part of a VCP submission, you have to include a statement about how you are fixing your procedures to avoid similar errors occurring going forward. As a rule of thumb, I think it is prudent to save everything you would have submitted as a VCP submission in a self-correction file, including a narrative description of the failure, how it occurred despite your reasonable procedures, and a description of how diligent you were in fixing the problem and correcting your procedures once you discovered the failure.