No, you're not being penalized.
As dmertz suggests above, Form 8889 is required to be reported to the IRS in this situation. And it's not available with the Free Edition.
According to the Instructions for Form 8889,
You must file Form 8889 if any of the following applies.
• You (or someone on your behalf, including your employer) made contributions for 2020 to your HSA.
• You received HSA distributions in 2020.
• You must include certain amounts in income because you failed to be an eligible individual during the testing period.
• You acquired an interest in an HSA because of the death of the account beneficiary.
