Your contribution limits should be limited your net profits less any deductible portion of self-employment taxes. I'm not certain why you are seeing something other than that. Did you enter your Roth IRA contribution amount before entering all your Schedule C data for both businesses?
Try closing your program if using the desktop version and then open up again and let any updates run. Then revisit the section.
Or you might try entering your contribution amounts under the traditional IRA section just as an experiment to see if your contributions are limited to your net earnings for both businesses. Then remove those entries.
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