Inverse modeling is strictly mole balance. The calculation does not take into account the saturation indices of minerals. If SI calcite is consistently above 0.0, it does not make thermodynamic sense that calcite is dissolving. I would look for other models if possible. SI(calcite) > 0 can be caused by silicate mineral dissolution, but most commonly by CO2 degassing before measuring the pH. So it could be a sampling problem. For most aquifer systems calcite is expected to be near equilibrium when calcite is present. I would not expect to see persistent supersaturation in an aquifer. Streams are another case, with diurnal cycles of respiration, temperature change, and CO2 degassing.