You need to look at your 1099-R. One possibility is that you withdrew $4000, had $400 of withholding, and received $3600 net. That should have $4000 in box 1 and $400 in box 4.
Another possibility is that you withdraw $4400, had $400 withheld, and received a net of $4000. Then your 1099-R should have $4400 in box 1 and $400 in box 4.
If your 1099-R is wrong you have to contact the broker for a corrected 1099. If it was case #1 where you withdrew $4000 and netted $3600, then it is, in fact, a $4000 withdrawal. The withholdings from box 4 go to your credit, but may not represent the total amount of tax owed, which depends on all your other income, deductions and credits.
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