We have been charged by our finance company x2 dishonour fees of $45 each and x3 car instalment payments of $57.59 as we did not advise them to cancel the direct debit all though we cancelled from our end with the bank and set up a AP through another bank. Can they charge us these payments all though we have paid the x3 instalments by automatic payments?

They can't collect twice for the same payments. Contact them and explain what happened and that the payments were made.

The dishonor fees are a different matter. You established a direct debit and didn't cancel it. So in essence those are your fault. Again, contact them and explain what happened and they may remove them. And be polite. An aggressive attitude probably won't help and you will have to eat the fees.