I am recounting my experience in the hope that it will help others in a similar predicament. I received a notice from the IRS stating that they had "adjusted" my refund, reducing it by about $4,000. "We changed the amount of self-employment tax on your tax return because there was an error on Schedule SE." When I called IRS I was told that I had made a computation error, which seemed odd as Turbotax had done all the calculations. I eventually reached an expert at the IRS on Schedule SE. She examined my return and realized that IRS had made an error, charging me twice for self-employment tax. The return was properly prepared by Turbotax. The IRS agent told me that she would enter the correction and that the IRS would pay me the portion of the refund improperly held back. Note that I have both W-2 income from a job and also income reported on various 1099-NEC and 1099-MISC forms from a sole-proprietor business. I declare this income on a Schedule C for the business. This is not the only time the IRS has made a bald-faced error that I have been able to get them to correct by calling.
