The IRS requires two Schedules C for a Qualified Joint Venture owned by a husband and wife (see reference below).
TurboTax should treat those businesses separately. Are you using the same business name and/or EIN number? That may be the issue. Add your first name at the end of the business name on your Schedule C and do the same for your spouse.
Also, delete (pencil icon) all entries related to startup costs. Then enter half of the cost on one Schedule C. You'll need to enter the amount over $5000 (half for each spouse) under Assets >> Amortizable Intangibles with a 15-year class life. This will record the amortization as a miscellaneous other expense.
For more information, see IRS Election for Husband and Wife Unincorporated Businesses.
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