Two examples that I can think of is that we (my wife and I) had oyster cards and arrived at Waterloo by National Rail from outside London and touched a reader at Waterloo that appeared to be for entry to the tube. Then probably touched it again at another barrier The cards got some stupid negative balance (£7.80 fare?), made various attempts to reclaim it at Waterloo but they told us to go to another office or something, so no luck with that....Do feel free to post details (in another thread maybe) of any issues you've had using Oyster at NR stations. If you've got a journey history scan that would help explain things. If the journey isn't too old you may still be able to get a refund from the helpdesk.
The negative balance triggered auto topup, but as the auto topup was old, my credit card had long since been cancelled so they sent me a couple of threatening emails before revoking the Oyster card, confiscating it when my wife tried to use it at Waterloo.
So we bought new Oyster cards after that.
Recently we went to London for the Jubilee boat pageant with a NR travelcard return. We went our separate ways unfortunately I still had my wife's ticket so when she went from Waterloo to CLJ she paid an Oyster fare for that. That brought the balance of the Oyster card too low, so she had to pay to get on the bus at Queenstown Road. But she got off at Queenstown road, and not Queenstown Road station as she was supposed to, so she paid again for another bus. Then at Battersea Park she topped up with £20 and tapped in at the Oyster reader there before travelling to Victoria. I checked the journey history at a reader at Victoria, Waterloo to CLJ was correctly charged but the Battersea Park - Victoria journey was showing as Victoria-Victoria, and charged at something like £4.30. I went to a ticket window to get it fixed but they told me to call the Oyster helpine. Haven't bothered yet.