When in doubt, always read the filing instructions.  Tax programs are only as good as you understand the law and tax rules because they all depend on your input.  You should also review the diagnostics because they give you clues as to what you may have missed.

In your case, you should have been prompted to make the input under Deductions > HSA/MSA/LTC Contracts (1099-SA, 5498-SA) > Health Savings Account (8889).  You need to at least enter a 1 for Type of coverage: 1=self only, 2=family.

Having said, that the omission shouldn't have caused the Box 12 amount to be picked as income.  It is very likely that you had coded the $3,555 incorrectly somewhere.