It happens when you clean up a scan with Adobe CS. I’ve had the same thing occur.
It’s just surprising that whoever did it didn’t flatten the image.
Nonsense. PDF vs. Adobe CS files are irrelevent. Straight scans are one layer, by definition, because they're bitmaps with no innate object definitions. The only way to get multiple scan layers is to do multiple scans, and even then they aren't going to segregate themselves by subject matter, since all the scanner sees is undifferentiated bitmap data.
If you have scan layers, without or especially with subject matter content differentiation, you have deliberate assembly, which in this case means tampering, because the document has no structural justification for anything other than a straight scan.