If a customer comes in and states that they received an ACH credit that they did not authorize, does this still qualify as an EFT error and become subject to EFT error resolution rules?

Yes.

So, if Customer A disputes a credit and after investigation we discover that the credit is a valid pre-authorized, reoccurring debit from Customer B's account with us, the resolution would be that it isn't an error? Apparently, the rest of the story is that A is owner financing a home to B and the EFT is for the payments. A wants to foreclose on B and wants to stop receiving the payments, which have been sporadic due to insufficient funds. We did not know this when the preauthorization was first given, however, my opinion is that we don't want to get involved by dishonoring a valid EFT authorization. Am I right?

NACHA rules don't require an authorization for credit entries if both the Receiver and the Originator are natural persons. And Regulation E doesn't have anything to offer except that Customer A has the right to dispute a credit entry to his account. The problem, as you've stated it, is that the transaction was authorized by the Originator (to be debited from his account).

I suggest that Customer A direct Customer B to stop initiating the credits. If Customer B fails to honor that, Customer A can effectively block them by getting a new account.