I made my HSA deductions, the software is reading it as it was my employer, and I am not getting the deduction. Why is there no way to fix this?

If the amount was reported on your W-2 in box 12 with code W, then it is labeled as employer contributions because it came through the employer's payroll system even if the only contributions came from your income.  This is also pre-tax money, so there is no tax deduction for contributions made through payroll deductions because you have already received the tax benefit.

If you made a separate contribution to the HSA outside of payroll deductions, then that amount is entered when you go through the Deductions and Credits > Medical > 1099-SA, HSA, MSA section of your return.