I've made all my own bubble counters, so I don't know how much of a problem this is with the commercial units. If you are making your own you can modify them to help make it easier to see the bubbles depending upon whether you want to use the counter on a system with a high or low bubble rate.
For a low rate you can get smaller bubbles (therefore more to count at a low flowrate) by making the opening in the tube that dispenses the bubbles smaller. Or at least making the opening smaller. Making the opening larger will yield larger bubbles, making a fast flow rate easier to count. The other thing you can do is make the tube for counting a lot longer, even 6-12 inches if you like. That way it's easier to see the bubble rise.
A final option is to check the gas flowrate off line. Run the CO2 from the needle valve into a pipet with a tiny bit of soap and water in it. Bubbles will form and rise through the pipet in a very controlled way. Use a larger pipet for measuring a higher flowrate. The only problem with this approach is that the flow into your reactor, which is likely under a bit of pressure, will not be identical to that used in your flowrate measurement. Still, you will be able to get a relative flowrate, which might be good enough.
There is yet another way of measuring gas flows. You take a container of know volume that is full of water, and invert it in a bath of water. Then you direct your gas flow into it and measure how long it takes to fill with gas. Problem with CO2 is though that it is so soluble in water you won't get an accurate measurement until the water becomes saturated in CO2.