Where do bad sectors come from?

I write to a DVD-R/W disk from Tivo for post processing on a Mac. My usual approach is to use MacTheRipper to transfer the contents to HD, where I modify it and write it back to a DVD-R.

The other day I tried this on a movie I had recorded and MTR said there were some intentionally bad sectors. Since the original write was an analog transfer, this baffled me, so I wrote another disk, tested it on the LiteOn and then on the Mac before trying the transfer to HD. Both playbacks were fine but I got the same error when trying to copy. I also tried directly copying the two VOB files and got read errors.

Does anybody have any idea what is going on here?