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Hi there, I know this thread is old but I'm having the exact same issue as you posted.
My W-2 only has box 12a code DD even though they deducted HSA to get to my net pay. I don't see any code W in box 12 and I don't think they subtracted my HSA contribution from box 1 of W-2.
Did you ever find a resolution for your question?
The resolution is the same for you now - you need to contact your employer to have them issue a corrected W-2. HSA contributions made must be reported with the code W to be correct. If your employer will not issue a corrected W2 you will need to contact the IRS.
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