If you were dealing with deposits to the partnership's accounts and the partnership was real under state law, the CTRs should only be filed with the partnership listed as a person on whose behalf the transaction was filed. "Criticized" can mean a lot of things, Compliance Mom, and not all criticisms are well-founded.
Whether the criticism came from an examiner or from an auditor, I don't think it was correct. If you had a "do over," I'd recommend a firm push-back on such a criticism, with a request for documentation of the examiner's or auditor's basis for his/her comment.
John S. Burnett
Fighting for Compliance since 1976
Bankers' Threads User #8