1. An FSA always covers both spouses... - Ok even though I'm not on her insurance, I'm technically covered by that FSA the same way she is by the HSA. Which causes this issue. Makes sense! - yes, kinda sort of...which is not to say that FSAs are otherwise similar to HSAs because they're not.
2. This means that while you are covered by the FSA, that you cannot contribute to your HSA... - I actually immediately halted my contributions to the HSA after we discovered having both isn't allowed. Shortly after her insurance began. - smart move!
5. The limiting factor is that you cannot use funds from both the FSA and the HSA for the same medical expenses. - Does this mean literally the same bill? You're not allowed to pay 50% of a prescription for the FSA and the other 50% from the HSA. If that's correct, we should be fine. She only put 90$ in that FSA and hasn't actually used it for anything. But the HSA has been used this year (solo) - Pay each billl with either HSA funds or FSA funds, not both. But note this:
"You must be able to receive the maximum amount of reimbursement (the amount you have elected to contribute for the year) at any time during the coverage period, regardless of the amount you have actually contributed. The maximum amount you can receive tax free is the total amount you elected to contribute to the health FSA for the year."
See https://www.irs.gov/publications/p969#en_US_2018_publink[phone number removed]
So you have access to entire FSA amount on January 1st even if you haven't paid it yet...also depending on your FSA plan, you may not be able to carry over much or any of the unspent FSA funds to the next year. Please read the section with the title "Balance in an FSA" at the link above, and spend all your FSA funds first.
6. Your coverage for the month is determined by the coverage on the first day of the month -So your spouse really started FSA coverage on January 15th? This would mean that you had HDHP coverage (without conflict) for one month or 1/12th of the year. In 2019, the annual HSA contribution limit for a couple with Family HDHP coverage (I assume that's what you have) is $7,000, so 1/12th is $583. If you (as owner of the HSA) are 55 or older by 12/31/2019, then you can add 1/12th of $1,000 to that amount ($83).
It looks like you're not talking about a lot of money, maybe 1 or 2 contributions too many. You may just choose to do nothing about the excess until you file your tax return in February (you file early, right? You should - less chance of identity theft). At that point TurboTax will walk you through the process in the HSA interview.
