It could be bruising from dull clippers but that looks like an infection to me. Cutting a plant can open it up to infection. Did you sterilize the clippers before taking the samples? If it looks like it is getting worse lower the RH in the tent to 40%. Perform surgery, sterilize your clippers and your hands for each cut, turn your fans off and carefully cut 1" below the infection cutting only the stem and remove the infected piece with as little disturbance as possible. You do not want to shake the spores off of the rot. Wait an hour before turning the fans back on. This will give the wound a little time to scab over.