I think it's more that the analogy is broken.

If I have a sheet of paper and I color a section black. That's it. It's black. No going back.

So I can see people thinking the same for PDFs. I drew the black box. It's black. Done. They don't realize they aren't dealing with a 2D sheet of paper, but with effectively a 3D stack of papers. That they didn't draw a black box on the page, they drew a black box above the page over the area they wanted to obscure.

The fact that this happens a lot is an indication that the software is wrong in this case. It doesn't conform to user expectations.