Hi YearOfTheBusOyster,
Sadly there are a lot of misconceptions in this post, some from TfL staff who really ought to know better.
So, the first thing to point out is that only adult Oyster cards with no discount entitlement go through the back office process overnight. This means that you won’t get a refund, sadly. It also means that sometimes it is cheaper to get a normal ticket with the railcard.
Helpline staff really ought to be aware that both Oyster and contactless charge extension fares, albeit that the Oyster ones are only calculated overnight. They also ought to know that Grays is not in zone 9 and that the caps are more expensive.
I can, however, explain how the charges were arrived at.
The first £6 counted towards the Anytime cap only.
The 2x £1.75 counted towards the Anytime and off-peak caps (and the bus cap, though that’s irrelevant here).
At this point the Anytime total was £9.50, just short of the £9.60 Anytime cap.
The £9.60 counted towards the Anytime and off-peak caps, but now they are the Grays ones of £28.60 and £14.05.
Finally the 95p took the off-peak travel up to £14.05 which was the off-peak cap.
I hope this helps a bit.