Yes, in a similar variant. The common theme was that the net effect was that the participant had zero unreimbursed expenses, yet had received an HRA reimbursement (it wouldn't matter if it was an FSA either).
The proper procedure is to have the employer attempt to recoup the now-overpayment from the participant. Failing that, the $1,000 in your example would be W-2 income subject to all regular payroll taxation (FICA, Medicare, FUTA, and possibly SUTA), and should be addressed via payroll processing and tax reporting.