1099-R: The amount of taxes withheld on your 1099-R is more than your taxable retirement income...?

My employer failed the 401k discrimination test and as a result money that was supposed to go to my retirement was sent back to me and taxe withheld.  The audit risk step in Turbotax is flagging a risk that:

 

"The amount of taxes withheld on your 1099-R is more than your taxable retirement income.  If you have an amount in Box 4 (Federal income Tax Withheld) of your 1099-R, generally all or part of your retirement distribution is taxable.  Go to Personal Income, and select the Retirement category.  Verify the amount in Box 2a of your 1099-R is the correct taxable amount."

 

I don't really know how to resolve this or what it means.  I simply entered my 1099-R as the form and boxes are complete on it.  The whole situation confuses me and I don't want it to be a problem.  Any thoughts or suggestions would be appreciated.