I suspect there is a mispricing here again.
The £3.9 fare is supposed to be “Travelling on London Underground and National Rail changing at Waterloo and Richmond (or Victoria, Clapham Junction and Richmond)” but in the Oyster system, I think that the Blackfriars OSI and other London Terminals OSI (except Vauxhall, E&C or Battersea) use the same code on the card. As a result, it is indistinguishable with a Waterloo interchange from the card.
Please complain to TfL and request a refund.