Form 1099-SA is about WITHDRAWING from an HSA. That has nothing to do with CONTRIBUTING to an HSA, which is what the program seems to be talking about.
Did you enter a W-2 that has a code "W" in Box 12? If so, that is the HSA contribution made through your employer, and is why you are seeing that.
Until you through the entire HSA section to verify that you qualify for an HSA contribution, the program will tell you that you made an excess contribution (because it thinks you don't qualify until you tell it that you do qualify).