I think the problem they are addressing is that acidification of the water will cause it to leach more minerals out of the surrounding rock. It is impossible to tell from this article, but I immediately question the scale of the experiment. In other words, do they take into account that the amount of CO2 they have bubbling through the core sample may be far more concentrated than what the aquifer would experience? This also brings up another issue: If a huge amount of the CO2 is bubbling up through the aquifer, then it really is not sequestered at all and will just reenter the atmosphere eventually.