Hi Fernando,
the ecoinvent database itself does not use the elementary flow called "carbon dioxide". The one that is in the database (carbon dioxide, Category: Emissions/Emissions to soil/ Emissions to soil, unspecified) has no characterization factor and is not used at all. Don't use this one! The ecoinvent database always uses "carbon dioxide (fossil)" or "carbon dioxide (biogenic)" (and some more). So please cross-check that you use those following the logic presented in the ecoinvent database. You might used the wrong one but due to the interoperability of the openLCA method package, it is accounted for in openLCA method package but not within the ecoinvent methods.
Hope this helps