If your system is relatively new, you could have seen an algae bloom. Algae loves nitrates, and often only show up once these nutrients build up to a certain level. In the new set-ups, you then often have a scenario of nitrates being available but the plants being too small to take it all up - especially on the size fish you have. One argument is that you can just wait for the system to go through maturity (the tilapia will not mind the water quality if the brown is just algae) or you can go after the algae (if that is the culprit). I always have a small UV sterilizer at hand for younger systems specifically for that initial "bloom". Have you tested water quality to rule out other issues?
Nate actually recommends 1lb of fish per linear foot of growing space. So with three 5 foot towers I have about 17lbs of fish to 15 linear feet of growing space. Just a bit more than he recommends, based on the fact that the towers cleaned the water so quickly once I put them in and stirred everything up, and then again when I added the fish and they stirred everything up... Im thinking it might be the algae growth... well im hoping. But I will shoot Nate a line all the same to see what he has to say.