After college, I had one student loan to pay back. It took three years to pay back the loan. About two years into making monthly payments, I received a letter from the bank stating I was in default and I should start paying back my student loan or else. Well, I called them and told them I had been making regular monthly payments and had receipts to prove my case. Good thing that I kept my receipts, the bank naturally blamed me, but the bank assigned my loan to another person. I was Actually paying for another student's loan. Finally after numerous Phone and letter debates, the bank admitted it had erred. Moral of my story is "keep your receipts".
You need to talk to your bank for clarification on this matter. If you were given the receipts after every payment you made, you can carry them and use them as evidence. It may be a system problem but you need to check on it immediately to avoid future problems.