I've had a similar experience with OFT. Thought they still owed me something like 300 dollars after I finished my course. Turned out to be my fault entirely; they only owed me 4 dollars or so. But I found out that they become very hard to communicate with once you've left the facilities. So make sure you settle your account before you leave (don't leave during the weekend when the financial staff's gone). I paid part of my balance with my credit card, despite the 2% uplift, knowing that, in case of trouble, I had the credit card company on my side.
OTOH - If you deposited more than 3000 dollars more than what you were planning to expend there, then something else must have gone wrong as well. So there must be more to that story than what's written here.