It would be wise for you to file an amended return.
1. The IRS gets a copy of the W-2C and will look for it to be reported
2. Your tax liability could be adjusted (if only slightly) for the corrected W-2, probably in your favor.
3. Since you did not "correct" the excess HSA on your original Federal Return, (you only paid the tax on it) the excess will show up again next year and you will again pay the 6% penalty tax. This will continue year after year and the correction in later years is much harder to do than the year after the excess contribution is made.
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