Not sure whether it was a fare anomaly or I was being an idiot:
I had a switch of office location in 2022 and my commute is now Surrey Quays/Canada Water – City Thameslink/Farringdon. Prior to EL opening, I was using LO – Jubilee – TL and getting off at either CTK/ZFD. However, I remembered I was being charged a NR-T fare if I used Surrey Quays, but only a TFL-LU fare if I used Canada Water instead.
I have stopped using this route since EL opened as the interchange walk at Whitechapel is shorter and I now go LO-XR(-TL) and still only get charged a TFL-LU fare as expected.