No, I've never received that message. The e-mail you receive informing you that your shop was accepted also says that the acceptance is subject to change upon further review. I presume that upon further review that there was something key missing from the shop and the report had to be excluded.
I don't know about every MSC, but several schedulers from a variety of them have told me that there is some leeway on shops, but it depends on the client. Some clients are more flexible than others. While I generally agree there is a breakdown of clear communication at some MSCs between the client manager, scheduler, etc, and the editor, and this results in the editor being incompetent, it does hurt all involved when a shop cannot be used. I believe they do try to use reports that are not perfect, but they know what a client will and will not accept. It's possible they initially thought whatever was wrong with yours wasn't a big deal and would be accepted by the client or the editor simply missed it, and it was not caught until it was sent to the client. It would be nice if they had informed you what was wrong so you could make sure it does not happen again. In fact, if I were you, I would respond with just that.
Never Complain, Never Explain.