Autopay accounts should always be separate. I opened a second checking account with my bank, and every month or so I make a deposit. That way if something like this happened it's not gonna get that much and its all separate
That might be worse - if the autopay amount is even a few dollars over what you put into the separate account, you'll be on the hook for an overdraft fee, which you _definitely_ won't be able to recover.
You can tell your bank to not approve overdrafts, at least in the states. They word it real weirdly at the bank, but you want to opt-out of the "overdraft protection" (the protection letting you purchase things you don't have money for).
That prevents overdraft charges, but not declined payment/NSF charges from the biller or your bank.
I don't really do autopay, but I've adopted using a separate account for all bills, and I explicitly move funds as I pay them (pretty easy these days with Zelle). I've since changed this out of laziness, but at one point I didn't even have a debit card attached to the account where my income is deposited to. (the financial equivalent of one-way data binding?)