If Cases are sending an auto-response from a User that is not defined as the Sent From (Email) in any of your rule entries, the auto-response may be coming from the "Default Response Template" setting.
Classic Steps:
Under Setup | Customize | Self-Service | Web-to-Case | Modify | Default Response Template
OR
Under Setup | Customize | Leads | Web-to-Lead | Default Response Template
The Default Response Template is not required, you can remove it if you do not want a response sent when no rule entries evaluate to True.
See also
Guidelines for Setting Up Web-to-Lead
Set Up Web-to-Case
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