The exact same thing happened to me. I left the filters on and it took a couple of day for it to clear out. That was the second time it had happened. The first time it happened I think I turned the filters off but I had messed something up in the tank setting up process and took the work I had doen uppart. I never got to see the results for the first one.
Should I have an air stone or anything in the tank? It's a 12 gallon and I have a whisper 20i in it. But the output of the filter is pretty much right at the water level so no bubbles or anything are made.