say it could possibly be bugs or more likely a ph issue. honestly need more info to give you a better analysis. if you're not checking your ph then it's most likely that, i get odd mutants like this sometimes with bugs but mostly its because i wasnt using the right ph when watering. those cups have drainage holes right? if not then there's ya problem but im going to assume there in the 2nd cup to catch the water and even then you dont want any water remaining in your dishes this also can cause ph problems.
actually on revision i think you might just need to get more oxygen to the roots by the looks of the way those cups are sitting they might not be getting enough fresh air. try just leaving them on plates so the holes at the bottom have direct contact to the outside air that may solve your problem. could also add some liquid 02 if you got it lying around, always a good thing. could maybe be a combo of things too but hopefully you'll be able to find an easy fix. i think just exposing the bottoms to more air a bit more will help..... also the thin plastic cups could allow a bit of light in and roots dont appreciate light.
