@tbar there used to be a line entry in TT that allowed you to enter the "employer HSA contribution NOT reported on a W2". It was used specifically for this instance where the employer (for whatever reason) omitted the some or all of the box 12 amount. Since your W2 taxable wages seem to be correct, you can enter the omitted amount directly into the program and it should appear on F8889, line 9 as required for employer pretax contribution.
