It's a known issue. Seen it on Google forums. Android still prefers Gmail (of course). Maybe it'll get better when we get upgraded from 1.6 (hope, hope). About the only fix is to actually delete the email account and re-install it. Not really worth it unless it's really lagging the phone. Just ignore the trash folder.
I'm starting to access my MSN mail through the browser. Nicer UI.
@queueman: I don't see where you can "check" emails in the other email client on the MTG3 in order to delete them. Even if you open each one and use the "delete" button, they still don't go away