If you have a reportable transaction on a business with multiple owners (say a partnership), do you have to list out each partner in section A as beneficiaries of that transaction.

No; a partnership is a formal business entity.

hmmmm, we were criticized for failing to file on each individual in a partnership and had to back file the CTR.

Compliance Mom, did they also make deposits into their personal accounts?

Was this a formal or informal partnership?

If the partnership is a legal entity, its owners should not be listed as persons on whose behalf the transaction was conducted when transactions are made on behalf of the partnership.

There is a ruling that suggests that you aggregate to report on the owner if entities are not operated separately and independently.

See FinCEN Ruling 2001-2

The particular transaction we were cited for only affected the partnership account.

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.