Code S in box 12 on your W-2 is not for an HSA, it is for a SIMPLE retirement plan. The HSA code is W.
"Code S—Employee salary reduction contributions under a section 408(p) SIMPLE plan. Show deferrals under a section 408(p) salary reduction SIMPLE retirement account. However, if the SIMPLE plan is part of a section 401(k) arrangement, use code D. If you are reporting prior year contributions under USERRA, see the TIP above Code D in Box 12—Codes. " See https://www.irs.gov/pub/irs-pdf/iw2w3.pdf
