Can a corporate demand for a repayment if they overpaid the workers’ bonuses for the last year?

My employer has "overpaid" a few workers' shift bonuses for the majority of 2013, and now corporate wants it back. They gave them 3 options; pay it in full, 3 payments or 12 week payroll deductions. There is some question as to how much is needed to pay back as they actually did work the "premium" schedule sporadically. The manager left the shift bonuses intact on purpose, because it was near impossible to change it in payroll system in a timely manner as the work load constantly changed and multiple work shifts were not always required. Sometimes the guys would work nights for a couple weeks and not earn premium pay, and then start back on normal hours only then to start earning it. If it was not a big deal and more convenient for the local HR to leave well enough alone at the time, can corporate really demand and enforce repayment? Especially since it was a known problem over a long period of time? If they start garnishing wages do the affected individuals have any recourse, legal or otherwise? It would seem in the best interest to sit down and work it out with each individual worker, especially considering the relative small amounts $800-$1200. I would say I'm shocked on how a huge Fortune 500 Corporation could be so clueless, but its my 3rd year in company, nothing surprises me anymore.