I think there are so many apples and oranges mixed up here that if we throw in some pears and cherries, we'll have a decent fruit salad.  I have never seen repayments to employers (or their disability insurers) shown on a 1099-SSA.  Social Security sends all the money to the beneficiary, who then writes a check, not to Social Security, for the repayment.  

What the 1099-SSA is telling you that the $28,868 includes $11,528 attributable to 2016.  The employer disability probably ran out in 2016, so that's the only amount that had to be paid back.  (Nothing was ever paid back to Social Security.  Got it?)  If the IRS notice of deficiency (which you haven't told us, when it was issued) included only the $17,340 in benefits attributable to 2017, then don't rock the boat.  Maybe they guessed that she was eligible for a deduction or "claim of right" adjustment for that amount, and were kind enough to allow it without even being asked.  

You tell us that "she was required to repay some of the benefits."  How much?  It's unlikely that it would be the same $11,528 amount.  But even if you want to admit liability for a greater amount than IRS assessed, you should have that number.