Well technically they are right. They are doing it last as it was not done when it was meant to. Oh yes and when they say doing it they mean correcting their stuff up.
I am not anywhere knowledgeable on these things but when my footings and pad was getting poured I questioned whether a car would fit between the house and the boundary and was told it was deceptive how much room there was. I asked if it was also deceptive that the boundary footings were 300mm in from the boundary.,..... they "do them last too"
Hang in there.... it how they deal with the issues that matters to be honest.