The Student Loans Company (SLC) has been continuing to take loan repayments for months after former students paid off their debts, it has been revealed.
About 57,000 graduates are waiting for refunds after excess payments were taken out of their wage packets.
Consumer organisation Which? discovered from a freedom of information request that £15m had been overpaid this year.
SLC said it could not work out the amounts repaid until employers filed their annual tax returns.
"The result is that there is a time lag," it explained in a statement, "And some borrowers nearing the end of their repayments are likely to overpay."
Dougie Mackintosh paid his loan off in June, but the £98 deductions were still being made four months later.
"When yet another payment came off in October I pretty much hit the ceiling," the Inverness-based 29 year old energy surveyor told the BBC.
Each month, Mr Mackintosh had complained about the extra repayments, only to be told that a "stop notice" had been sent to the tax office, HM Revenue & Customs (HMRC), which manages the deductions from pay.
But HMRC claimed to have heard nothing from SLC.
"It's a complete disgrace," said Mr Mackintosh. "They seem to be totally incompetent."
The £15m overpaid by former students to SLC this year is up from £9m in 2009.
Which? found some ex-students were still having deductions made 11 months after their loans were repaid.
Others have had to wait long periods to have their money refunded. In one case, it took six months for the funds to be returned and even then some of the refund was missing.
Mr Mackintosh's problems have become even worse.
Last weekend he received a further letter from the loans company, informing him that they would start deductions from his salary shortly. Yet his whole debt had already been cleared.
"I need the full pay packet for buying Christmas presents, and now it's as if I hadn't been paying in the first place."
SLC has revamped the system so that former students can switch their repayments to direct debit in the last two years of repaying their loans, and it has asked 68,000 eligible ex-students if they'd like to make the change.
"Switching to direct debit means you can choose your monthly repayment date and we can make sure your repayments stop at exactly the right time," SLC said.
Which? is urging SLC to ensure that former students are not kept in debt for longer than they need to be.
"Paying off a debt is a stressful experience," says Which? chief executive Peter Vicary-Smith, "So the last thing people need is to find that they've been paying out more than they needed to."