By this article, some of the unindexed files could be file attachments... https://support.office.com/en-us/article/Unindexed-items-in-Content-Search-in-Office-365-d1691de4-ca0d-446f-a0d0-373a4fc8487b?wt.mc_id=o365_portal_mmaven&ui=en-US&rs=en-US&ad=US