First, the 1099-SA has nothing to do with contributions. When you have excess contributions, that means that more money was put into your HSA by you, your employer, anyone on the planet who is eligible, than your annual HSA contribution limit allowed.
The amount with code W in box 12 on your W-2 is the total amount that your employer AND you contributed to your HSA through payroll deduction, Because your payroll deductions are included in this amount, many taxpayers think that they should enter their payroll deductions as personal contributions, but no, they are part of what the IRS calls the "employer" contribution.
"For both instances I indicated that I contributed zero " - so it does not matter what YOU personally contributed, what matters is how much was contributed to your HSA from any source.
NOTE: whether or not you enter (we say "enter", not "submit") a 1099-SA has nothing to do with excess contributions.
Please tell us what kind of HDHP coverage you had in 2021 (Family, Self-only, None), for how many months, and whether or not you are filing married joint and whether or not you or your spouse have other health coverage.
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