The medicare wages and tips box of your W-2 is supposed to be the same your wages, tips, other compensation box. All this means is that your medicare tax is based on 100% of your earnings. Now, if there is a difference, it could be that you have a 401K, or 403K. If you add the amount from your 401 or 403 to box 1, it would probably equal box 5. If it doesn't, I would contact your employer's payroll department.
How does your Medicare Wages (box 5) affect your tax filing?
Your employer is required to withhold Medicare and Social Security taxes based upon your wages.
If you do not have enough withheld, you will need to pay the deficient amount when you file your income tax return.
If you have too much withheld, you may be able to get a refund on your personal tax return if your withholdings occurred because your employer withheld too much.
Please see the following link for more information on the tax rates.
Social Security and Medicare Withholding Rates
More information if you are subject to the Additional Medicare Tax
More information for uncollected Social Security and Medicare taxes