If the stock was held short term and you would have had a capital gain if sold instead of donated, that limits your donation amount to the FMV minus unrecognized short term capital gain.
For long term stock, the FMV is used for the donation.
The program needs to know both of these answers to correctly figure the calculation if it is short term. No correction should be made.
See:
Do I need a receipt?
IRS Pub 526
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