From what I have read above, I would guess you have your bubbles per second set very close to the ragged edge of what your fish will tolerate. I have run into this a few times where the fish start complaining (gulping air) when I have the bubble count too high (again, we are talking 3.5 bps vs 3 bps). As for the end of tank dump, a good 2 stage (assuming you have one) will prevent end of tank dump). You should be able to run your tank down to 0 psi without dumping excess cO2 into the tank. Myself and others have run their 2 stage regulators down to less than 100psi without problems.
As to how to prevent it, maybe lower your bps flow slightly.
As to how to prevent it, maybe lower your bps flow slightly.