Hi Chris,
The free walkthough at Southwark is implimented by setting fares for destinations to Southwark via Waterloo East. I don’t think anyone would expect people to walk through both which is why they haven’t defined a fare. Where no fare is defined there is a secret formula to produce a fare which usually ends up at the NR1-T rate.
The OSIs will have joined everything up but there is no route between Southwark and Stockwell via Waterloo East so it didn’t charge the extra 10p. But you are right, Oyster won’t refund a previously charged fare so you were left with the original zone 1 NR1-T fare.