Here's what the Manual tells IRS to do.  I would reply to the 106C with a copy of the W-2 in question.  If there was withholding on other forms, send them also and a summary of how they total the amount claimed on the return.  Shouldn't be something that a GS-12 in Appeals needs to be looking at, but with IRS you never know.  

https://www.irs.gov/irm/part21/irm_21-005-003r#idm139932262630416