I could not reproduce this situation with a regular database connection managed by Auth0. However, you mention that your users are stored in your MongoDB so I’m assuming this may be a custom database connection.
For a custom database connection if you try to perform the verification email flow you’ll likely get an error about a missing verification script which is not available for configuration through the Dashboard. If you proceed to configure that custom script through the Management API have in mind that your logic in the script may influence the outcome of the verification procedure. For example, if I coded a custom verification script that returned a negative outcome (aka called the callback function indicating that the verification process was not completed) then I did obtain that error message.
If you’re in the above situation then troubleshoot your script to ensure that it correctly signals that the email was updated to verified for an existing user.