Were there any conflicts or controversies with Sigmund Freud's discovery?

Yes. My favorite is his analysis of the washer woman who had numb hands. Freud, using neuroanatomy, showed that neither damage to the peripheral nerves nor the central nerves could account for her numb hands, and therefore, the problem was psychogenic (that may be the wrong Word). The local academy of neurology loved his explanation. Of course, today, we recognize that carpal tunnel syndrome is not an effect caused by the nerves but by the bone. The nerves merely report the narrowing of the passage through the bone.