I wasn't able to put my finger on it. Avatar wiki says:
Pandora's toxic atmosphere is unbreathable by humans due to the presence of high concentrations of carbon dioxide (>18%) and hydrogen sulfide (>1%).
However, entire planet seemed to be covered in plants, including water plants. Earth isn't half as green as Pandora is, but it still has pretty low levels of carbon dioxide (0.035%) even with all the emissions that come from human society.
I understand about the air toxicity due to other chemicals found in the atmosphere, but if the plants are performing photosynthesis, shouldn't it be enough to keep the atmosphere relatively free of carbon dioxide?