Your question is confusing because you said you decided to let the contribution ride and apply it to this year, but you also have a 1099-SA with code 2. Code 2 indicates you asked for a return of excess contributions. Did you in fact ask for a return of excess from your HSA bank in 2025? Was that request made before or after April 15, 2025?
Start by looking at your 2024 return. Do you have form 5329? If you did not have an excess contribution before 2024, then lines 42-46 will be blank, line 47 is the excess that you did not remove (or told Turbotax you did not remove) line 48 is the amount that will carry forward to 2025, and line 49 is the penalty.
