Hi Kt,
Quick answer is that you were charged correctly, but not for the reasons given.
Where a travelcard plugs a hole between two extension fares you are charged the cheaper of the whole fare without the travelcard or the two extension fares. In this case the fares are National Rail rather than Underground so zone 1 peak is £3.10 which covers London Bridge to Vauxhall. Then the zone 4 extension is £2.60 which comes out at £5.70. As this is more than the £4.60 whole fare you are charged the whole fare.
The gold card discount applies to off-peak fares and the off-peak cap, but you didn’t reach the discounted off peak cap of £7.25. This is one of the drawbacks of travel in the afternoon peak which is included in the page When Not To Use Oyster.
I hope this helps you to understand what happened.