Is a bank allowed to charge a fee on a disputed ATM, POS,ACH transaction?

It depends on the situation. In your ATM example, if the customer disputes ever performing the transaction, then it would seem doubtful that you could charge the ATM fee to the customer. But, if the customer disputed a $200 ATM transaction by saying that s/he really withdrew $20, and the bank normally charges a set amount to access the ATM regardless of amount, then I'd say as long as the fee is disclosed properly, the bank can charge the fee.

The same logic would flow for a Point-of-sale transfer. If customer asserts transaction was unauthorized in its entirety, you can't charge the fee for the transaction.

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If customer asserts transaction was unauthorized in its entirety, you can't charge the fee for the transaction.

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Matt hit the nail on the head here. You need to make the customer whole. If you give them back funds from an unauthorized transaction, how could you justify charging them a fee?

Take a look at the Commentary of Reg E - Section 205.11(c)-3. It states the financial institution may not impose a charge related to any aspect of the error resolution process (including charges for documentation or for investigations).

Actually, that's not exactly what it says. The reference is in comment 3 to §205.11(c).

If the customer is correct and the error occurred, you are prohibited from charging a fee for the process, and you have to put the customer back where he was before the error took place, refunding any fees and crediting interest.

If, however, the customer is incorrect and the transaction is not an error, you may exact a fee if you've previously disclosed it and if the fee is not so large as to have a "chilling effect" on a customer's good faith assertion of error claims.

So you can be safe in assuming that error resolution will never be a profit center for your bank!