Oh dear.
To withdraw mistaken contributions, you must make a special request to the HSA bank. It may require a special form, it is not a regular withdrawal. If you did request a withdrawal of mistaken contributions, the HSA bank must issue a corrected 1099-SA. If you requested a normal withdrawal, then you made a major mistake with significant tax implications. Because this is a regular withdrawal, it is taxable unless you have offsetting medical expenses. Any part that is not covered by offsetting medical expenses is an improper withdrawal and is added to your taxable income plus a 20% penalty.
Then, you need to go back and file an amended 2019 return, to change your answer to the fact that you did not remove the excess contributions before the deadline. It will still be added to your taxable income but you will also be assessed a 6% penalty. For 2020, there would be a continuation of the 6% penalty, but since you spent down the account and closed it, the penalty is 6% of the remaining balance which is zero.
