The Taxpayer Advocate has a page explaining this letter, which states:  "The letter should explain why they disallowed part of the claim."  Does it?

The issue is $1,800 withholding on a W-2?  Is there anything unusual about the W-2?  Handwritten?   Withholding is a large percentage of the total wages?  

The TA page indicates you should explain why you disagree, while asking that if your explanation is not accepted they forward the case to Appeals.  You have two years to resolve the problem, without going to court. 

https://www.taxpayeradvocate.irs.gov/notices/letter-106-c/