Auto-Tune adds a slight delay, as a necessary process in identifying the pitch. If you select data for processing it must start and end in silence, or else you will hear clicks where the delayed sound is preceded by zeros and the ending sound is discontinuous with the unprocessed sound.

Another cause for clicks in the data is artifacts in the original sound file. Examine the waveform of the sound file under the highest possible magnification. If you see a large number of "spikes" or other unusual shapes that were otherwise inaudible, Auto-Tune may attempt to tune these artifacts, creating the clicks.