More often than not, the problem with "challenging" a regulatory agency or individual examiner is that the issue at hand has a level of subjectivity involved. Examiners' statements often can be subjectively interpreted -- e.g., the analysis of the loan-loss reserve needs to be "improved", an earnings policy or interest-rate risk policy requires "enhancement", or an OFAC new-customer opening process needs "improvement".
It is always fair and warranted to ask that an examiner's suggestion be made more specific in scope, to permit you to properly enact the desired control features.
Just being polite and nice in your retort, as suggested above, is assumed; but what is important is being able to competently and persuasively articulate an objective response which convinces the examiner-in-charge that you have and will continue to enact reasonable and prudent controls. The EIC is your audience; you're presenting your issue to him/her, not to the recommending examiner. Keeping your eyes and eye contact with the EIC makes it clear that he/she ultimately has to decide the relevance of the examiner's recommendation.
An examiner prior to October 1, 2003, recommended the bank engage "an automated process to perform all PATRIOT Act-required SDN listing matching". At the exit meeting the examiner-in-charge tended to back up the examiner. The bank staffperson involved was able to professionally outline the steps already taken; she pointed out that the SDN matching was already occurring using a less expensive process consisting of an Internet fee-based/per-event identifier system; and she convinced the examiner-in-charge that our actions already taken were more than reasonable for our size institution. The EIC then stated he'd review the issue, and prior to leaving the bank and out of earshot of the examiner, he stated that the matter was reviewed and that we could ignore the earlier recommendation.
Just being nice and polite doesn't do it alone. It's being able to present the issue persuasively, to build and promote respect. We all hate the word -- selling -- but that's the key. It's not important that they like you; it's important that they respect you. Sincere, persuasive, professional points that are made, and which show you are committed, will always garner the respect of the examiner-in-charge.
And there's always the ombudsman route if you're passionate and prepared to lay all of your cards on the table.