Recently, We have enabled Mailbox for all CRM Users to use Server-Side Synchronization for Incoming/Outgoing Email.

We have one process in place when Email Activity is created and Lead is populate as Regarding in Email Activity, We are updating Lead from Plugin.
After Enabling Mailbox, Few Leads (Disqualified/Qualified) are Re-open by System User and few Auto Reply Email Sync Back to CRM with new Email Activity Create when we Enable Mailbox.

I am not sure if anyone has faced this kind of issue.

Thank in Advance.