An example journey is Crayford to Canning Town which is charged as a zone 3-6 journey. If you change between DLR and Jubilee line at Canary Wharf you'll be charged for zone 2-6, but the difference will be adjusted after touch out at Canning Town in the way described.
Thanks for clarifying! So you're talking about making an Out-of-Station Interchange at a location B that costs more to reach than the final destination C (from your origin A), where you obviously get deducted the A-B fare when touching out at B, and then due to limitations the Oyster system is not able to immediately refund you down to the lower A-C fare when you touch out at C, so instead you get the refund processed overnight.
As a side note, personally I think TfL is being too generous with this policy, and it would be better to leave people with the A-B charge (or rather charge them for whichever is highest out of A-B,B-C and A-C), both on Oyster and contactless. This is because all* fares are meant to be based on the zones and modes used, and so a person travelling A-B and B-C as part of their journey probably made use of enough zones and modes that an A-B or B-C charge (or more!) is warranted. The lack of a correspondingly high A-C fare coded into the system to trigger if the passenger has passed through B is presumably due to TfL not having realised that passengers might travel A-B-C, rather than a deliberate attempt to discount that route. While this oversight would likely just yield a small revenue loss (e.g. the price of an extra zone) for reasonable B, it presents an opportunity for people to abuse the system with unreasonable B, and get away with paying for a short journey when in actuality they've gone somewhere far away, done something useful outside the station during an OSI, and returned back to somewhere near their origin (taking care to stay within the maximum journey time). (For an extreme example, it looks like a peak Watford Junction - Euston NR -OSI- Euston LU -OSI- Euston NR - Watford Junction - Watford High Street journey would be charged just £1.90. And would a Heathrow T5 Rail - Paddington NR (not HEX) -OSI- Paddington LU -OSI- Paddington NR (not HEX) - Heathrow T23 Rail journey be free?)
*One notable exception is the special off-peak discount for travelling into Zone 1 in the afternoon peak, for which a refund at the final destination in Z1 should still be given.