The sad thing is that this should be simple for any company to do. When HR departments make stupid mistakes like this, it ends up costing you at the end of the year (I know it ends up being the same amount of money, but it is much easier to just have it taken from your pay than to pay it out of pocket). Luckily, I have never owed any federal taxes at the end of the year, just a little here and there for state and local but it is usually less than 100 bucks for both my wife and I at the end of the year.