If you did not contribute the annual maximum through your employer, indicating that you personally contributed an additional amount reduced your taxable income by the difference between the amount contributed through the employer and the annual maximum. The amount that you indicated was personally contributed above the annual maximum was penalized 6%, but apparently the reduction in tax for the deduction that brought your contributions up to the annual maximum was greater, resulting a lower tax bill than without the erroneous entry.
For example, for an individual under age 55 who has single HDHP coverage, the annual limit for 2022 was $3,650. If you contributed $2,000 through your employer and erroneously said that you contributed $2,000 personally, you would get a reduction in taxable income of $1,650 and a penalty on $350. Assuming that you are in the 22% tax bracket, the reduction in taxable income would be 22% of $1,650 or $363 and you would have a penalty of 6% or $350 or $21, resulting in a net reduction in your calculated tax liability of $342.
