Youtube could easily curb the wrongful/overzealous take down notices by indicating that:
1) Access to our API for automated take downs is a privilege.
2) Too keep your privilege in good standing, no more than 3 false positives (reviewed by our human staff) per calendar year.
3) If this limit is exceeded, then API access is revoked and claims are now required by to be submmitted by certified/registered mail, one per envelope (starting at ~US$5.58 per letter).