Another snag Iโ€™ve run into while using Mu4e was that sometimes I also use Appleโ€™s Mail on macOS and iOS and any messages I delete there would only be flagged as โ€œtrashedโ€ in Mu4e, so they would show up in the inbox, cluttering things considerably. The fix for this was to set Expunge Both in my .mbsyncrc file. Also much better! That one has been bugging me for a long time.

Source: A couple of Mu4e improvements | Baty.net