code w is what went into the HSA.
on the 1099-SA that's what was taken out which needs to be reported.
code 1 is a normal distribution and should not affect your taxes
and code w should not affect your taxes since the wages on line 1 should have been be reduced
if anything one would expect taxes to go up.
we can't see your return so double check w-2 and 1099-sa entries
also the entries for 8889. you didn't enter the code w amounts on the 8889 did you - that's doulble dipping
so also check you 88889 entries.