Prob just your bennies. I brew microbial tea each week that is pitch black and add a couple gallons to my netpots, it stains the roots brown and there's always some funky colonies hanging out down there. As long as you've got lots of oxygen, don't worry, just let them do their work. IMO, If you use lots of bennies, the water should almost look like its boiling from all the air you're pumping through. If its just a few bubbles here and there, take off your airstone and run an open line, you'll get great movement (I stopped using airstones a couple years ago, and my results have never been better)
If you get real root rot, you'll know it. Your plants will start to look very unhappy, then you'll smell what seems like rotten potatoes (potatoes are roots). When you look at your roots you'll see patches of slimy, dark brown, very thin roots, some will be almost black. When you touch them they fall away from the rest as they're dead.