Cole cash register operators don't enter PLU number persay any more in relation to fruit or vegetable as they use in effect touch screen computers which display pictures of fruit and vegetable produce instead. I suggest that what @TheBBG outlined is correct and that they did not have to honour their price scanning policy, that being the first free item being free and remainder charged correctly.
Coles would argue that the PLU is in effect the image on the cashier's screen (e.g. another apple variety) and it was operator error and not scan error. Maybe Coles (and Woollies) need to update their policy to cover the recent technological changes at their checkouts.
The wording in their policies comes from the Supermarkets Scanning Code of Practice. Maybe the wording in the Supermarkets Scanning Code of Practice also needs updating by the Australian Retailer's Association.
It is likely their resolution of offering only the difference in product cost met their own policy (noting for my first post I assumed the apples had a barcode and were scanned as this was what was outlined in the original post).
Furthermore, when making a complaint, it is important to be civil and unemotional. As soon as one becomes uncivil or emotional/angry, they are only likely to do the bare minimum to resolve.
It is also worth noting that I have had an experience at Woollies whereby loose discounted fruit price at the checkout was not the same price as that shown in store. When advising the cashier, she immediately gave me the product for nothing even though the sale had not been completed (I expected manual price adjustment and for me to pay the correct price). It did make my day to save a few dollars and possibly should have raced back in store to fill a bag before the error was corrected to get more freebees (unfortunately while I did think it was possible at the time, I'm not that sort of person).