Hi Gavin,
I suspect you’re not going to be alone in finding these sort of discrepancies.
Firstly it’s important to explain that any fares for journeys beyond the zonal area are set by the train companies, in this case Greater Anglia. Even if there is a problem with a particular fare, TfL can’t just fix it. Fares are currently set to be updated three times a year, in March, July and November. If the fare is set by TfL then they can make changes at those times, but if it is set by a train company then the company has to agree the change.
In terms of the fares to Canary Wharf, I suspect that Greater Anglia are pricing the Elizabeth line fare as just a National Rail fare while those using the Jubilee line or the DLR attract a premium. I’m not certain that they should be treating the EL route that way as the Paddington to Abbey Wood line is treated as a tube like line. However, for now they are so you can benefit. If you wish to complain about the premium being added for the short zone 2 hops from Stratford then you’d need to write to Greater Anglia.
Splitting the journey by using two credit cards is certainly one way of reducing the premium addon because the TfL fares within the zones are cheaper. The drawback is that you run the risk of not capping correctly if you decide to make any other journeys in the evening, for example. You might also try exiting through a gate at Stratford and then coming back in again using the same card. That should split the journey in two but still preserve the tally towards a cap should you need it. Note that it MUST be a gate rather than a platform validator.
I think you’re lucky if TfL have refunded you this time. I wouldn’t want to raise hopes that it will always happen, particularly if you ask yourself several times.