So yeah, I immediately brought this to Payroll's attention in March, got promptly ignored, followed up, barely got a response 2 days before my contract ends… asking for £1800 in repayment. Yeah fuck this, I'm not working the last 2 days of this contract.
(For the record, I had set aside what I thought was the overpayment — they just informed me days before leaving that I was mistaken and actually owe nearly double what I have set aside.)