Firstly those gates at Waterloo are a major nightmare. You aren’t the only person who thinks they’ve touched into the Underground because you’ve already gone down steps from the National Rail station.
Forgive my confusion but can you clarify. You tried to let them know where the incomplete touch was but were told in an email that there was a problem. Then you saw another message saying you could pick up a refund by using your card? Does this mean you have a refund queued? If you have then read my new bit about Faster Universal Load on the topping up page.
Otherwise perhaps you could clarify what you have done and what and how you’ve been told.