It's the infected/dead part I cut off. I only posted a picture to see if anyone can identify what caused it. The rest of the plant appears to be healthy, so I didn't see any point in posting pictures of it.

It looks like rot to me as well. Its really tough to get rid of, but cutting off all infected areas is a good way to control it, but ultimately its still around. I bought a Catt. skinneri years ago that had come from an infected batch and I'm pretty sure I doused it in Physan (follow instructions), cut off all infected parts (I kept cutting until there was only green left in the tissue) and kept it on the dry side for the rest of the growing season. It recovered nicely and showed no signs of rot the next year.

I would cut another bulb off of your plant to be sure.