@joshbierman
Adding income to a tax return can have side effects besides the direct tax on the added income. The increase in income could reduce or eliminate various deductions or credits that are not related to the income that was added, but that have income-based limits or phase-outs. If you received Social Security benefits it could make more of your Social Security taxable. These side effects are in addition to the self-employment tax.
To figure out why it's reducing your refund so much you have to compare your entire Form 1040 line by line before and after adding the 1099-NEC to see what else is changing besides the 1099-NEC income. If there's a change in an amount that comes from another form or schedule, you have to look at that form or schedule to see what's happening.
