Payment and tds not matching

It is valid. TDS should be deducted in the month in which bill is raised or service is provided or receipt whichever is earlier. Hence even though payment is made in next year, it is treated as valid. But if the payment was not made or there was any breach in the contract then such TDS deducted can be claimed back.

Having difficulty explaing because entry of payment is in bank account on JUN, 2016. TDS shows in Form 16 of previous FY.

There is no rule that payment should be made to creditor/employee in year of TDS deduction..