It depends on the origin of the CO2 source. If the emission is from biogenic origin then you can exclude otherwise need to include it in the LCA analysis.
Normally the conversion factor for biogenic emissions of CO2 is zero.
(1 kg of Biogenic CO2 = 0 kg of CO2 equivalent)
This aspect may have some consequences on the inventory, e.g. for CO2 emission from biomass combustion, if in the life cycle inventory you consider CO2 emissions as biogenic, you have not to include the CO2 absorption during the biomass growing.
Another detail which could be taken in consideration is methane, as well as some other hydrocarbons featuring GWP, generated during combustion process. In spite of the biogenic nature of carbon (if so), they should be considered on anthropogenic side.