Refund issues

I've used Turbo Tax for many years. This year has not been a good experience. 

1. It said I over paid my HSA by over $11,000. I double checked all of my entries and could not figure out why it says that.

2. I was supposed to get over $500 back in federal and what was deposited into my acct was a little over $300.

3. I still have not received my state taxes.

4. It's says I owe for the whole year of 2023 for city taxes and I did not start working in the city until September 2023.