RMD Penalty

I have five IRA annuities.  On four I took more RMD than was required.  On the fifth one I took less than was shown for that RMD.  However, the total that I withdrew came to a little over the total that was required for all five.  And yet, Turbotax is showing that I owe a penalty of over $400 tax on excess accumulations in my retirement account after I enter that fifth RMD.  If the total is covered why would I be penalized?