I received a cashiers check from a customer. After I deposited in MY bank the check was returned from issuing bank with stop payment. Customer claims he paid his bank with a check that bounced, so the issuing bank put a stop payment on their own check. Issuing bank have not specified why or who put a stop payment on check. Can a bank put a stop payment on their own cashiers check when they discover they issued a check paid with a bad check? Can a customer put a stop payment on a cashiers check for which he has received goods or services?
There is no dispute about the goods or services. The customer is just a crook.

If your state has adopted the model knowledge of the Uniform Commercial Code, the following statute applies.

§ 3-411. REFUSAL TO PAY CASHIER'S CHECKS, TELLER'S CHECKS, AND CERTIFIED CHECKS.
(a) In this section, "obligated bank" means the acceptor of a certified check or the issuer of a cashier's check or teller's check bought from the issuer.
(b) If the obligated bank wrongfully (i) refuses to pay a cashier's check or certified check, (ii) stops payment of a teller's check, or (iii) refuses to pay a dishonored teller's check, the person asserting the right to enforce the check is entitled to compensation for expenses and loss of interest resulting from the nonpayment and may recover consequential damages if the obligated bank refuses to pay after receiving notice of particular circumstances giving rise to the damages.
(c) Expenses or consequential damages under subsection (b) are not recoverable if the refusal of the obligated bank to pay occurs because (i) the bank suspends payments, (ii) the obligated bank asserts a claim or defense of the bank that it has reasonable grounds to believe is available against the person entitled to enforce the instrument, (iii) the obligated bank has a reasonable doubt whether the person demanding payment is the person entitled to enforce the instrument, or (iv) payment is prohibited by law.

If "the crook's" story is to be believed, the bank allowed "the crook" to purchase Cashier's Check with uncollected funds. Unfortunately for the bank, it was stck with "the crook's" bad check. Now the bank is trying to cover a potential loss by refusing to pay it's own Cashier's Check. As long as the check was originally presented soonerthan 90 days from it's issue date, it cannot legally do this, and you can sue for damages.

If "the crook" lied to you and actually gave you a stolen/counterfeit Cashier's Check, then the bank should have stamped it as such, as opposed to Stop Payment.

In the second story, the bank has no obligation to honor the check because it never actually issued it.