No, you do not make changes to your 401(k) contribution amount. Just enter the W-2 as shown. Since you are taking the correct actions, you can ignore the excess messages. 401(k) excess deferrals don’t cause a penalty to be calculated on your return like an excess contribution to an IRA.
Please be aware, that if you do not take out the excess amount by April 15th (your plan fails to return the excess by April 15th), then you are taxed twice on the excess deferral left in the plan. This happens once when you contribute it and again when you receive it as a distribution. You can't include the excess amount in the cost of the contract even though you included it in your income.
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