Hello mizcue,
We're glad you thought to ask Apple Support Communities about the issue you're having with missing an email in the Mail app, but seeing it when you sign in to the webmail provider area. If you haven't already, quit the Mail app and restart your iPhone to see if fresh connections help: Restart your iPhone
If not, and if the account is not a POP account, remove it and add it back to see if it starts syncing as expected. Those steps can be found under "Remove your email account and set it up again" here: If you can't receive email on your iPhone, iPad, or iPod touch
Let us know how it goes.
Take care.