I’ve seen this happen a few times, an email message just will not delete. Clicking the trash can shows the message delete animation, but the message just reappears behind the animation. The same thing happens in list view. The solution is to reboot the phone, everything should be fine after a restart.
To reboot the phone, hold the wake button for several seconds. A slider will come up asking you to power off. Shut it down, wait a second or two and then press wake to turn it back on. Your email should work normally.
I’ve found rebooting every few days is a good way to clear any slightly odd behavior or minor slowdowns. iPhone is a 1.0 release and these are software bugs. I’m confident they’ll be fixed in a future update.
Update: Force-quitting Mail can also help. To force-quit any iPhone application, just hold the home button for about 10 seconds, until the home screen displays.