The zone 1-2 cap is a cap on charges for travel solely within zones 1-2. If you use zone 3 then your cap becomes zone 1-3. Yes, your single fares between zones 1-3 have contributed towards a zone 1-2 cap, but you still have to pay for the zone 3 bits. These are called extension fares and are calculated at the same rate as the fares just for the extension bit. If the extension fares plus the smaller cap end up being more than the larger cap then the larger cap is charged.
It doesn’t matter when the zone 1-3 journeys are made, they will never fully contribute to the zone 1-2 cap.