No one agrees with every decision. Disagreements are fine; it's what you do when you disagree that matters.
Show that you were professional. Show that you raised your concerns in a productive way. If you have an example that proves you can effect change, great -- and if you don't, show that you can support a decision even though you think it's wrong (as long as it's not unethical, immoral, etc.). Show that you can agree to disagree.
Every company wants employees willing to be honest and forthright, to share concerns and issues ... but to also get behind a decision and support it as if they agreed, even if they didn't.
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