Aatrix is recognizing $118,500 as a prior year's limit which is true, that was the 2016 limit.  

The 2017 limit was increased to $127,200 for 2017:

The employee should have continued to be taxed up to the 2017 limit because those wages beyond 118,500.00 are still taxable.  

Create a Historic entry to correct box 3 (and 4 if necessary) using the steps in the W-2 wizard: