Could give details to your experiment?

I did a greenhouse experiment in Bonn, Germany but the soil samples were from Ugandan wetlands. Among the 54 soil samples 27 were under flooded and 27 were under field capacity condition and I had collected gas samples 3 days per week. I had used static gas chamber method

First I would say you need to consider the fact that flooded does not equal anaerobic, since oxygen will difuse into water and from it to the rest of the soil environment. Another issue to look into is that if there is nitrate available, denitification (NO3 to gaseous N2) will also produce CO2.  What about autotrophic organisms? Could it be that they thrived in the samples under field capacity conditions taking up CO2? As you see, these are some wild guesses, but worth looking at and maybe discarding them.

Thank you Rafael

Thank you very much "Kenneth M Towe". It is not really.

I can see two possibilities:

1: the emission of CO2 from the flooding water ( if too much CO2 is dissoved in the water, as happened in most groundwater or stream water)

2: birch effect

I am not sure of the hydrology of the location you collected the samples from, but the CO2 may also be due to the dissolution of carbonates. If the water you are adding is acidic (which probably is), and the location you collected the material from was alkaline, the CO2 may be coming from carbonates.