"In 2023, they screwed up yet again, only underwitholding by $160. "
I take this to mean that your employer contributed an amount equal to your annual HSA contribution limit less $160, so this $160 should have been applied to reduce your carryover of excess contributions.
So, yes, the $160 should have been on line 43 (the 5329 instructions say "Line 43: If contributions to your HSAs for 2023 (line 2 of Form 8889, Health Savings Accounts (HSAs)) were less than your contribution limit for HSAs, enter the difference on line 43.")
Then line 45 should be $160. And line 46 should be (329-160) $169. And Line 47 should be zero, so line 48 should be $169.
Then the penalty on your excess should be 6% of the smaller of line 48 or the value of your HSA on December 31, 2023, so in this case, $10?
Does this match your situation? @dmertz is right that the 5329 needs work and that the change you noticed was the result of the latest code update. Let me pass this on.
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