We discuss the treatment of the systematic frequency shifts due to microwave lensing and distributed cavity phase in Heavner et al 2014 Metrologia 51 174-82. We explain that the microwave lensing frequency shift is generally non-zero and finite in the limit of no applied microwave field. This systematic error was incorrectly treated and we find that it contributes a significant frequency offset. Accounting for this shift implies that the measured microwave amplitude dependence (e.g. due to microwave leakage) is comparable to the total reported inaccuracy. We also discuss the importance of vertically aligning the fountain perpendicular to the axis of the cavity feeds, when the cavity has only two independent feeds. Finally, we note that background gas collisions have a different behavior for cold clock atoms than for clock atoms at room-temperature, and therefore room temperature measurements do not directly apply to laser-cooled clocks.