Even when storing using the browser extension, some sites confuse 1Password into submitting the Sign Up form rather than Log In.
Mint is one example that will consistently fail: https://wwws.mint.com/login.event. Notice how the autofill hotkey returns a form error asking you to confirm the e-mail address, meaning either the wrong fields were populated or the wrong submit button was chosen.
This also happens on Runkeeper. Same situation.