This is an older post but in case someone finds it looking for an answer...
If a little popping noise or digital click happens at the end of a clip where you faded out completely, try zooming way in and slicing off a little sliver of the end of the clip. Readjust the fade. Or, you can zoom in and highlight a little sliver of the end of the clip and click 'silence' under 'editing'. This often does the trick.