My T. knuthianus has the same scarring, and it seems to occur when it has growth spurts. It's growing in a hothouse, so it doesn't get direct sun but it does get good light. It occurred when I increased watering with the onset of summer, so I still wonder if it is an infection-related thing or just rapid expansion of the stem diameter.
At first I freaked because I thought that it had insects or rot deep in the folds that knuthis have, but they just seem to callus over and the plant grows happily enough. My one initial attempt to lever a black mark out of the fold quickly made me realise that it was firmly attached to the stem.
From what I can figure the underlying tissue is healthy and firm, and I just leave it alone. If it's anything like my cereus that once scarred over after getting a rotten aureola, one day the scarred tissue will just drop away as the stems grows, leaving a healthy surface underneath.
If they don't fall away, I would just accept it as a part of the growing architecture of the plant.
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