yes it looks like heat damage, the clear bottles should be filled as high as possible to avoid that little hot zone between the stalk and the side of the bottle. If they're still rooting, try a place without direct sun at the height of the day.

-s

If they lack water for a large enough time (due to lack of enough water or due to root rot), the trunk can wrinkle. At the moment, it seems unsightly but, that is all. I assume you have not had rot issues in that area or with the roots before? In the future, any time you suspect root rot, use the pin prick method in the soft or darkened areas to see if you get nice white sap or not. Avoid watering when dorman, if the soil is already moist or if the potting mix holds too much humidity.

The soil was to the very top. The damaged area was benith the soil. Where it starts is where the soil was.

Ah sorry I missed that you pointed that out in your original post...luis has good advice above, if you suspect rot then you can act accordingly. If the growing tip looks okay then I would just wait and observe. Every couple of weeks check for progression or regression to rot and you should know where it is going soon.

Your puckered part actually looks mild and you have no discoloration at the puckered area, could just be thirsty from the rooting process. How does the growing tip look?

-s