Deductions & credits

I assume that you (i.e., the two of you) contributed up to the Family limit ($7,300) to your spouse's HSA and up to the Self-only limit ($3,650) to your HSA (although it does not matter if you put all the money into the same HSA). Since the two of you would share the Family limit, it often happens that taxpayers in this situation would overcontribute by about $3,000.

It does not matter from which W-2 these contributions come from. It does not matter who made the excess contributions - you get to chose who (you should have seen the question near the end of the HSA interview asking you who made the excess contribution, but this really means: who is going to have the excess withdrawn?

Generally, you want to withdraw as much of the excess by the due date of the return as possible. As noted above, it does not matter from whose HSA it comes (or if it comes from more than one).

The amount that you cannot withdraw (usually because there is no money left in the HSA(s)) is carried over to next year. Yes, this is penalized at 6%. However, it is very easy for people still under HDHP coverage to discharge the carryover. In the next year, the HSA contribution limit is reduced by the amount of the carryover. This means that the taxpayer needs to reduce the amount of contributions to the HSA in the next year that he/she would have otherwise contributed. With a little discipline and understanding of the system, this will permanently eliminate the carryover with a minimum of expense.

When TurboTax determines that you have excess HSA contributions derived from employer contributions, the excess is added back to Other Income. This is because employer contributions are removed from Wages in boxes 1, 3, and 5 before your W-2 is printed. Since you can't benefit from excess HSA contributions, the excess contributions have to be added back to income. 

Therefore, the amount (the excess contribution) that the HSA custodian sends to you is not an income item. You won't be taxed on it again.

Make sense?