This happens when changing the tempo of an audio file with the Time & Pitch Machine, if the tempo of longer stereo audio files (interleaved or split stereo) is changed less than one bpm (e.g. from 120 to 120.9 bpm).
Solution
This happens only with time stretching algorithm Version 5. This version of the algorithm cannot process very subtle tempo changes on stereo files.
Use one of the Logic 6 Time & Pitch Machine algorithms for subtle tempo processing.