This is my second grow, with the first harvest about 7 months ago. I thought I cleaned all my gear well. My plant started dipping a root into the nute solution about 5 days ago. This morning, I noticed they were much more brown than they should be. I did a flush thoroughly cleaned the whole rig again with clorox. My stone and its air hose were slimy and there was some form of sediment / slime on the inside of my reservoir. I think this was the beginnings of some form of root rot. After the flush and clean, the roots look much better.
TLDR: Check your roots often.