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"fossil" fuel locked up ancient CO2 - putting it back 'now' is, apparently, the problem.
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The problem is balance, yes it was originally in the atmosphere, plants used to it leave and produce oxygen, animals used the oxygen to eat the plants and put the carbon back in the air. Plants formed a balance with the animals so enough carbon is in the air for the plants and enough oxygen is in the air for the animals.
Humans are putting too much CO2 back in the air too quickly (or at least this is the idea) and there are less plants to counter it.
Places where balance has failed are deserts.