Hi Chris,
Neither. The default fare is a zone 3-4 fare which would be charged if you changed at Custom House and Canning Town. When you exited at Canary Wharf you were in zone 2 so you were charged a zone 2-4 fare. The system can’t give you back what it’s already taken, but when the journeys are put through the back office it will queue a 10p refund. Unless you become eligible for another £1.40 you won’t get it until 2 weeks have passed, but you will get it back.