Actually, at the time, the atmosphere had less CO2 than now in it, because all that carbon was trapped in those dead plants. For one reason or another, a lot of dead plants did not decompose (whether there wasn’t a bacteria that ate them, or because they sank to the bottom of the oceans, or many other reasons).
Eventually, when the world biome and geography got to a place for those plant corpses to decompose, the CO2 level in the atmosphere went up, although some of the carbon was trapped in underground deposits that have become oil and natural gas deposits.
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