Hi Matthew,
This does seem like a strange one. When you transfer products from one Oyster card to another the original one gets cancelled. The card itself still appears active but the next time it is touched in on a journey it will be physically cancelled. However, the central system should know that it’s been cancelled and not allow anything further to be processed against the card.
I can’t see what rule you might have broken though. You have pointed out the three travelcards to them which should have raised alarm bells. And if they’ve refunded the travelcard from the wrong card then that is down to them. Also, an Oyster card is not supposed to be able to hold more than £90 in credit, but I guess it might allow it if the top-up is coming from a transfer.
What you do now is up to your conscience, really. When the travelcards expire the card will start using the PAYG balance.