I just got off the line with a CRA rep for an estate (died Christmas day 2022) where the payment for the Jan 2023 GST/HST Credit and Climate Action Incentive payments were added to the instalment account.
As of Feb 28, CRA’s system should apply the payment to outstanding amounts BEFORE issuing a refund.
Nice to know those calls should no longer be necessary.
I had a client who owed about $7,000 in Canada Child benefit.
She was making $500 per month payments against the debt (via online banking as a payment to CRA Family Benefits) but after about 6 months she noticed they would direct deposit the $500 back to her bank account each month. The correspondence showed it as an “over payment” so she just stopped paying them. She hasn’t made a payment in about a year now. Her account still shows about $4,500 in CTB still owing to them. 
Maybe I should recommend she attempt to pay again and see if the CRA can get it figured out this time.