ProSeires typically defaults to using the Tuition and Fees for a tax credit vs making the 1099-Q earnings tax free. There is a way that you can change the amounts available to make the expenses offset the 1099-Q earnings. 

1. Open the Dependent Student Info Worksheet for the son. 
2. Scroll down to part VI - Education Expenses. 
3. Look for line 17: Used for credit or deduction. This is probably the full amount of the expenses in the first column. If so, then ProSeries is trying to use the expenses to give them a tax credit. If you reduce this amount then it will 'free up' the expenses to offset the 1099-Q earnings.