My normal workflow is to edit video in Premiere and import the sequense with dynamic link in After Effects to add effects.
In several versions of Creative Cloud it has been a problem, that when I edit my Premiere sequense the audio won't update. For example if I place a new clip in a sequense with an interview, the old audio still plays but the visuals are changed. Really anoying and the only way to come around it is to delete media cache files in Premiere and After Effects.
In the new versions of After effects a new problem has occured. If you have a sequense in Premiere where there is "empty holes" in the audio timeline then After Effects "loops" the sound from the clip before. Only workaround is to place audio on all of the timeline and turn volume totally down.