This is exactly why I don't do auto payments. Would you rather fight to get your money back from a utility bill mess up, or refuse to pay it before it is fixed?
This costs the company money and a lot of paperwork, so the threat of doing it is often enough to get them to sort themselves out.
Too: even when getting a direct deposit authorization for an account, you are almost always (US) also allowing withdrawals from your account, in the event the depositor claims they made a deposit in error.
Increasingly, banks seem less secure and more porous when it comes to holding my money.
I don't pay any bills manually; all of them (utilities/heating/electricity, mobile, internet, kindergarten, insurance, creditcard invoice) happen automagically - I just review online how much was paid and how much I have left :)
I typically spend about 1 minute per month paying bills.