Apart from intake air, the compressor itself may be a source of CO2. During the first few hours of operation some compressor filters will remove CO2. But this CO2 will be released into the compressed air once the filter becomes saturated with water, causing CO2 levels to increase. This is why a monitoring plan is crucial to ensuring your filters are regularly maintained to prevent filter degradation.
Other filters will also convert the much more dangerous Carbon Monoxide (CO) to CO2. This is so minute though, that it will not cause a failure.
Is your compressor running too hot? Could it be due to poor ventilation? The life of the filter cartridge is affected by high temperatures and can degrade increasing chances for CO2 contamination. Ultimately, for most compressors, filters simply cannot be relied upon to remove CO2.