This is odd, we know that this may happen so we have introduced a mechanism of remembering the last password generated for certain domain. If you generated a password with our plugin on some website, but you didn't save it, then once you reach login dialog on that website and we autofill originally stored credentials you should see pop up saying if you want to use generated password instead of the one you have stored in your passwords storage.
Could you please be more explicit wit the scenario - website and description of the initial state (feel free to PM me) so we can investigate if the process works OK for that case?