I think it is. Preview used to correctly handle the thing, and now it doesn't. Users cannot be expected to inspect the raw PS code of their PDFs to determine standards compliance. What they can do is assume that something that works yesterday, and appears to work today, is in fact working.

The PDFs didn't change, the application did. It's the application's fault.

If you have compatible behavior that you remove, it's on you to alert the user of the reduced functionality.

The PDF that FineReader made worked properly. The one that Preview made didn't.

But by this logic, no software other than those that Apple sells you directly (their own or through the MAS) is "supported software". If Apple makes a change and all of them break rendering it useless of anyone using software not bought from them, would you still be making this same apology?

It's not clear if the issue is caused by the PDF files produced by ABBYY, or if the issue is also present in other OCR'ed PDF files.

In either case, Preview shouldn't silently corrupt the file. It could display an error saying that it was unable to save the file, or a warning that some data couldn't be saved, so that the user can check if the file still works for them after saving.