Retirement tax questions

The amount in box 2a is most definitely not correct on my 1099-R, and this page on my broker's site says they commonly do this:  https://www.betterment.com/resources/common-tax-form-questions/#16  

 

The 1099-R is for excess contributions withdrawn, and boxes 1 and 2a have the same value.  Box 2a should only have the earnings reported on it, which is about 1/10th of the amount withdrawn.  If I enter box 2a exactly as in in Turbo Tax, the only follow up question is if it's a "qualified disaster" deduction.  So it doesn't handle the situation.  

 

The Betterment advice in the link above is to do form 8606, but when I reach that section in TT, it tells me to OMIT the amounts from the 1099-R section.

 

The only other option I see is to do a "substitute" 1099-R in TT.  But I'm not sure if that's right.  This situation doesn't seem like it should be so uncommon.  I did the same thing with Vanguard and their form had the right amount in 2a.  Not sure why Betterment couldn't do the calculation.  

 

CORRECTION: I realized why (I think) the brokerages did this differently.  With Betterment, I had converted the contributions to a Roth from Traditional IRA before I withdrew the excess.  With Vanguard it went straight into a Roth and then was removed.  However, the Traditional IRA contributions I made with Betterment were from already-taxed income before they were converted to a Roth, so removing them should not re-tax them.  I'm just not sure how to indicate this to the IRS without simply changing the amount in box 2a, which you've said not to do.  

 

Can you help?