Yes, CO2 is hygroscopic and it will dissolve into the water, and pull water into the tubing. I've seen it go 1 inch /hour through 6 feet of tubing. I think the concept with the CO2 controller is that it will keep operating at the CO2 set point. You obviously overshot your setpoint, and then the controller had to shut off for an extended period. The controller should be operating "ON" at least half the time, then this won't happen. A check valve at the reactor is still a very good idea, for those times the system is OFF, for instance when your CO2 tank is empty and you are getting a new one.
There needs to be a needle valve and a check valve in the controller line.