Why does making Traditional IRA contributions for 2016 and 2017 and then doing Roth IRA conversion cause taxable income?

My 1099-R 

box 1 Gross Distribution - $11,000

Box 2a Taxable Amount - $11,000

Box 2b Taxable amount not determined - Checked.


5,500 of that is 2016,and 5,500 is 2017.  Is this 1099-R just wrong, or is there some way for me to mark half of this as 2016?  If I put $11,000 for 2017 donation it fixes the math but says I'll pay a penalty for excess contribution.