Billing of a merchant became my problem

I write with utter disgust, I have been a standard bank client for many years and after this incident, I feel like leaving.

My story is as follows:

I filled up for petrol at about 2.5 weeks ago, I received an SMS saying that this has come off my account. Together with that I have made many other swipes using my cheque card and referring to the balance that I have on my app.

As such I had a positive balance on my account. 2 days ago i logged onto my banking app and have noticed that I am now in a negative balance.

When questioned the call center agent at first he had no clue. However as the call progressed, he started telling me that i will now incur charges and interest on my negative balance and the reason for this is because Caltex submitted their billing at a later stage.

I would like to know how does this become my fault when I had received an SMS confirming that this has been paid.

I wish not to be charged nor interest on this account.