as you noted Form 945 is to report withholding on payments reported on nonpayroll forms such as Form 1099.
https://www.irs.gov/forms-pubs/about-form-945
sorry. but even if you do have a filing requirement, it seems Turbotax's Quick Employer Forms does not include this.
https://quickemployerforms.intuit.com/faq.htm
an S-Corp distribution would normally only be reported on your K-1 not a 1099. The exception to this would be an S-Corp that was a C-corp making a C-corp dividend payment, but then 945 would only be required if you withheld taxes on dividend payment.
review your filings with the iRS. perhaps you incorrectly reported withholding on the wrong line of a form.
if you did, that form may require amending. if no such error, I would suggest filing the form and checking box A.
