It's a result of the possibility of having a layered structure in PDF files.
Any vector painting program (e.g. Inkscape or Illustrator) will do the same.
One way to avoid this has been done in the horowitz report, where the original redacted pdf was converted to images (or printed out and scanned back in).
Those images then were OCR'd and the resulting text embedded on top of the scanned images in the PDF, which led to all those artifacts anons found.