The main reason people get the 'excess HSA contribution' error is because the HSA is entered with the W-2 entry, and then it gets entered again in the HSA interview in TurboTax.
That may be what happened to you. You are right that you may want to enter your W-2 manually, instead of importing it, if you feel the importing may be causing a problem.
If you use TurboTax Online, it is always best to close the program, clear Cache and Cookies, and then return to the section you were working on. Sometimes using a different browser will help, too. Data can get 'stuck' and not clear/close properly!
Here's more info on Excess HSA Contribution.
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