Auto-filing e-mails on Cases: Mail content not shown under details and attachment with extension .unknown created
Regarding the ".unknown", you can update the list of extensions it recognizes at Administer - System Settings - Safe File Extensions.

Regarding the rest that isn't how it used to work. Not sure if something's changed recently or maybe there is something unusual about those emails. You say it's both html and plain - are all the emails coming from the same source or different types of sources, e.g. MS Exchange, gmail, etc.

UPDATE: https://lab.civicrm.org/dev/core/issues/940