I found the same issue upon filing my 2017 tax return. My husband was on a regular medical plan prior Sep 2016. In Sep 2016, his company started to offer HDHP and he switched to family HDHP (kids are under his plan, so it's family). He was told that he could catch up the contribution and he put $5951.25 in 2016. I've always had self-only HDHP and contributed $3240 in 2016. While filing 2016 tax return with turbotax, I was not told there's excessive $2441 contribution.
Now I'm filing 2017 tax return. Again, I'm on self-only HDHP (I put $3240 in 2017) while my husband is on family HDHP plan (and he put $6750 in 2017). This time I was told by turbotax that we have excessive contribution $3240 in 2017 and $2441 in 2016. I STARTED TO REALIZE THAT that IRS considers that both of us were covered under a Family Plan, even of myself was on a Self-only HDHP and so the TOTAL max allowed HSA contribution was only $6750.
To avoid extra 6% penalty, turbotax suggested to withdraw $3240 from either of our HSA account by 04/15/2018. But turbotax said there's nothing I can do for the excessive $2441 contribution in 2016. I then reviewed my 2016 tax return report and found that we're already charged $146 ($2441x0.06) in 2016 (I didn't realized it until now).
So my question is what can I do to my "not-intended" mistake in 2016 tax return? I wanted to withdraw $2441 to prevent any ongoing penalty. Please advise. I've signed to use turbotax live (paid $179) and would like to get the professional assistance from a CPA. Thnak you very much.