Schedule SE is prepared automatically when you indicate that you had income that is subject to self-employment tax. This will usually be accompanied by a schedule C for a small business. Your net profit from your small business or independent contractor status flows to form 1040 where is combined with your other income and subject income tax, and the net profit from self-employment also flows to schedule SE to calculate self-employment tax.
It sounds like you had income from a 1099-MISC or a 1099-NEC and did not report it as self-employment income. You may need to file an amended tax return to report the income as self-employment but first, you must determine if the IRS is correct. Did you receive income on a 1099 and was it from a hobby or a business?
If the income was from a hobby, you don’t need to pay self-employment tax, but you may need to send an IRS a letter to convince them that this was a hobby rather than a business. If this was from a business, then you do owe self-employment tax, but, if you file a schedule C, you will be able to deduct your business expenses against the income. That would reduce the amount of self-employment tax that you owe.
