We need to file a CTR for a reportable transaction that involves one of our Bank Cashier's checks.
Cashier check payable to bank customer cashed by POA, do we indicate our customer in section Section A and then list the POA as Individual conducting transaction in section B?
We do not know that our customer received the benefit of the cash POA was the only one present at check cashing.
Is the CTR simply completed with one section A naming the POA as the one who received the cash?

I would file it like your first suggestion.
Did the POA sign as a POA? Then he/she did it on the customer's behalf. I don't believe you have to prove who benefited, but to the best of your knowledge the customer did, and the way you completed the CTR indicates that as well.
It's like a signer cashing a check from where they work, payable to cash, and saying they are doing it for the company. You go by what they tell you.

I agree, we would indicate the customer, not the POA benefited from the cash.