PROBLEM:
Here's why I think you are saying.
Your employer contributed to your HSA for you.
They have reported some small amount on your W2 in box 12 (look for an amount with code letter W).
This is automatically captured by the TurboTax program when you are done entering your W2.
You were shown an easily missed message to complete the HSA interview to claim the HSA deduction.
You did not complete the HSA interview.
You are now being told that your HSA is over funded.
SOLUTION:
Find the section in the Turbotax program for Medical Deductions and Credits.
Look there for a part about HSA/MSA Contributions.
Work through this interview answering all questions.
If you don't know an answer, stop and ask questions before entering a guess.
