K9-Mail does not detect PGP encrypted mail automatically
I have the same problem when sending encrypted mails from my Apple Mail client with GPGMail2 plug-in.

Apparently K9-Mail supports only PGP/Inline and not PGP/MIME which seems to be the standard formatting PGP-Emails today.

If you like to test it on your own, configure GPGMail to use inline mode through your Terminal:

defaults write org.gpgtools.gpgmail UseOpenPGPInlineToSend -bool YES


Reference.

There is an open feature request to address this issue. Hopefully, the K9 developers will fix this soon. So, consider starring this issue.