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Maybe I'm confused or he was...isn't it treated like income and thereby adjusting your AGI? He might have had other tax situations that made him pay rather than receive a refund that I didn't ask about.
Maybe it was the additional 5% needed to satisfy the tax on just the $38K, that caused him to owe money (single filer). In the OP's case, the guy would be short another 5% in taxes on $120K (as a married/jointly filer) if it's separate like I think you are alluding to.
If he owed money it was because he miscalculated what he should have taken out.
If you're going to get a $2,000 on a $90K salary and you do a 401K withdraw, it doesn't change the math on your taxes with regard to the $90K. If you, however, don't take out the appropriate amount, given your other forms of income (in the case of my example, your $90K) and your deductions, etc. then you may end up taking out far too little on the $38K, in which case it will come due at tax time.
But again, that has everything to do with withholding too little and nothing to do with it impacting his normal refund. It's just the fact that somebody taking cashing out $20K while making $35K will be taxed against it differently than somebody taking out $20K while making $150K.
It might push you to a level where some of the tax deductions phase out.
For example, If the guy had a kid and got the child tax credit, but then the 401k withdrawal pushed him up to where he lost the tax credit, it would actually cost him more than the marginal rate on the 401k money.
Also, if the 401k didn't withhold enough for his tax bracket, then he could face a pretty substantial bill in April.