question about on time payments and ach

I just have a general question about afterpay and bank payments. Lets say you pay by ach but when they take the payment out there is no funds in the account after the day you paid Would that still count as a missed payment even though you paid on the due date, and your bank didn't have those funds? Or after a few days, would you be able to pay the balance and still have your total amount without losing your spending limit?