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There are a number of possibilities here:
Even though you submitted your returns if you owed in excess of $1,000 with the return you could have been penalized for not paying in sufficient taxes during the year.
You could have missed an income item or two thereby creating additional taxes. The IRS would have corrected this and sent a billing.
You could have included all income but entered one or more items incorrectly. This could generate additional billing.
You could have lumped Social Security and Medicare taxes with Federal withholding. These are not to be included there and would have generated an additional billing.
Please start by checking these items to see that all items have been correctly addressed. If they were, please return to me and we will be able to proceed from that point. Also, please let me know the reason the IRS is stating for the billing. They are usually quite clear about this. After all, it is possible they are wrong.