Yes, you are correct that your Self-Employment Health Insurance Deduction should be limited to the repayment amount.
Did you enter your 1095-A info only and indicate that it was self-employment insurance in that section? If so, you should not enter it anywhere else in TurboTax.
If you're using TurboTax Online, you could delete your 1095-A, close TurboTax, clear your Cache and Cookies, re-open TurboTax and re-enter your 1095-A.
Since we can't see your return in this forum, let us know if this doesn't resolve your issue.
Here's more info on How to Enter 1095-A.
@misko22
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