When CO2 is added to a tank, it normally increases or decreases the pH, (I cannot remember which.) However, as most people have plants in tanks with Co2 injections...the plants absorb the Co2. Yet when there is no light, the plants stop growing - and absorbing Co2. Therefore, the Co2 level will countinue to rise with no stop, having a potentially negative effect on the fish.
As Aquatic-Store mentioned, some people just time their air pump to pop on when the lights go off, so as to increase surface agitation and diffuse more Co2 from the water into the air and replace it with oxygen. However, this is a waste of Co2 - not that it is all that expensive though.