A Nutrafin system (the kind with the little ladder thing, right?) is a yeast-based system (the pressurized systems are lots more expensive and have a metal canister that you get filled with co2) and it's virtually impossible to get too much Co2 into the tank with those, so that probably isn't the issue. If you can give us ammonia, nitrite, and nitrate levels, as well as info on tank size and stocking, maybe we can figure out what's wrong.
Good luck!