Surface agitation is necessary for proper gas exchange to occur. At night, the plants are not expelling 02 since there is no light for photosynthesis to occur. That causes a greater buildup of CO2 in the water, and without enough surface agitation, the buildup is too great for the fish to overcome. Either put your CO2 on a timer or run your CO2 off of a PH controller. You can then put your outlet back below the water-line for proper water movement, and more efficient use of CO2.