When 3 people come in on behalf of an entity to withdrawal money for the entity, we have been listing the entity as the beneficiary and the transactors as the 3 people. It is local farmer's market and we know the transactors are not the beneficiaries. It is not a multiple transaction since it is only 1 amount withdrawn. That means we have 3 part Bs and only 1 Part A.

I am sure that isn't correct, since we are to count the transactors as beneficiaries, but that is how my boss thinks we should file the CTR. Any help on how to handle this scenerio?

If you have knowledge that the transactors are not benefitting from this withdrawal, then your boss is correct. The entity that is benefitting goes in section A, and the three poeple making the withdrawal go in section B.

i would list the one individual conducting the transaction in Section B. I'm assuming the other 2 came along as a security measure? that's my opinion.

Yes, they send 3 for security measures, but only one is at the teller window.

In that case, I agree with nemsi - just list the one who conducted the transaction.