I'm not sure what a "BOT" filter is -- I haven't seen this acronym before.
The CO2 should get dissolved better by your filter. However, there are two exceptions to this. One, if the filter is not sealed, and has a lot of turbulence to it, you can lose CO2 that way. For example, if you have an uncovered wet/dry filter, you lose significant amounts of CO2 as the water cascades over bioballs. Similarly, if you have a hang on tank power filter (HOT), and it splashes significantly, you'll drive off the CO2. Both of these may drive off CO2 that is not directly injected (and both can be mitigated by a secure cover, and minimising splash; keeping the tank full for a HOT filter makes CO2 loss negligible).
Secondly, if you're pushing A LOT of CO2 into your filter, you can detrimentally effect the bacteria in there and inhibit anaerobic decay. In the case of some canister filters, injecting CO2 in there over a long term may reduce the lifespan of O-Rings and other seals. Eep.
Though a fairly uncommon occurrence, depending on what your media is, you can also damage or dissolve it -- obviously, anything that acids will eat would be a bad idea.