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Yes. Too much surface movement will allow the CO2 to out gas, to escape to the atmosphere.
Some people run a bubbler on a timer, to turn it on for a few hours at night. Turn it off well before the lights come on so the CO2 can build up to a good level to get the plants going strongly when the light comes on. Mostly these are for tanks with pressurized CO2.
Usually DIY CO2 is not so productive that you need to run a bubbler at all.
If your filter provides some rippling at the surface that is usually plenty to help with oxygen levels and keeping surface scum under control.
 
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