The most important thing to determine is WHAT you measured the temperature OF. If you measured the temperature of the bag, then the temperature will be higher for the carbon dioxide bag. That’s because the carbon dioxide is trapping the heat, and thus, it heats up. Therefore, your thermometer was probably in thermal contact with the bag, measuring its temperature.

When most people do this experiment, they cannot get good thermal contact between the bag and the thermometer. Thus, they usually end up measuring the temperature of the air BELOW the bag. That air will be COOLER in the carbon dioxide run, because the carbon dioxide has absorbed a lot of energy from the light, resulting in LESS energy for heating the air below the bag.