Mine always has some amount of bubble, even at night. I think it’s because other gases will also come out of the water to fuel the bubble, but they also get purged out during overflow. If you’re using a controller, maybe someone else can answer whether you have to periodically purge it manually.
The reactor will fill more with water when the CO2 is off, and when it is on the bubble will increase with the outflow limiting it to a maximum size. I think you’re worrying a bit too much about the bubble. Many people use the stainless version and they can’t even see the bubble. If you dial in the concentration of CO2 that you want, and it’s staying steady from lights on to lights off, then you’re good.