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In our experience, nobody is ever unhappy when the correction is an upside for the employee.
Our best advice is to be completely transparent, communicate how the error occurred, what steps you have taken to make sure it doesn’t happen again, how you have audited the rest of the organization to make sure there are no other issues, and how you plan to correct the error (ie. retro-pay).
Of course there may be some tax implications associated with this retro pay, depending on the amount in question; this should be discussed with the employee(s) directly, and every accommodation should be made to maximize the benefit for the employee.
If you and your team are direct in your communication, this “error” should actually go a long way in fostering more trust with HR instead of the opposite.