Exclusion from wages. 

You can exclude up to $5,250 of educational assistance you provide to an employee under an educational assistance program from the employee's wages each year.

Assistance over $5,250. 

If you don't have an educational assistance plan, or you provide an employee with assistance exceeding $5,250, you must include the value of these benefits as wages, . . .

If that doesn't work, attach a statement to the return explaining why there is no entry on Schedule 1, LIne 8 or elsewhere that would add this in and then subtract it out.  Keep the statement handy if the taxpayer receives an IRS letter, so you can send it to them again. 

The payment was more than $5,250?  Ask for a corrected W-2, or add it to Wages with a Form 4852.