"In any case, he filled out forms that allowed for a distribution of $540 and the "mistake" box is checked. The form doesn't say where the money was going."
Was this a form for a "Mistaken Distribution"? Has the HSA custodian asked for the return of the $540?
Otherwise, perhaps it was a form for a "mistaken contribution". If so, the HSA custodian should have sent the money to your husband. Please check your transactions in the HSA account...was the $540 ever sent anywhere? If it was sent to his employer, then fine - you won't report it or pay tax on it.
"Can that $500 be included as already-taxed income on his W2 and if so, how would we know" - unfair question on my part, since you can't tell just by looking at the W-2 (the code W amount is removed from Wages in boxes 1, 3, and 5, so everything looks the same no matter how much is removed).
"The bank suprevisor said we will get a check for $40 from someone (them or employer?) that we pay taxes on. But that's the same $40 the W2 has included in Box 12!" So the HSA custodian (is that who you mean by "bank supervisor"?) is acknowledging that $40 is an excess contribution and they are returning that to you. That's OK, because your husband had that withheld from his payroll (which removed it from tax), and it you get it back because it was an excess, then you should (1) get a check for $40, and (2) pay tax on that.
"Question is..who is considered to have made the withdrawal? Him or his employer?" I don't know, which is why I have asked you to go look at your transaction history to see if the employer has taken the money back.
"Filing a 8889 that doesn't match the 5498 worries me" - Now that you remind me that you have 2 HSAs, this is even a better reason not to be concerned about the 5498-SA. The 5498-SA is a multi-year look at an HSA, so it's not unusual for the 8889 to not exactly sync with the 5498-SA. Even better when you have two HSA's, because this means that you have two 5498-SA forms (you do, don't you? Did he make contributions to both HSAs in 2021?).
As for the $40, was it deposited twice into the HSA? Or is it just that it was reported as deposited twice: once as part of the code W on a W-2 and once on the 5498-SA. If the latter, then ignore it. Keep good records of what you are doing and why in case anyone ever asks. This is a confused situation not of your making. As I noted above, we just want your return to be as accurate as possible. If you run through TurboTax and get TurboTax to say that you have a $40 excess, then this is good - just say that you will withdraw the $40 by April 18th (I guess this is true since the HSA custodian told you they are sending you the check, right?), the $40 will be added to Other Income on line 8 on Schedule 1 (1040), and you will pay tax on that (but no penalty). If this is where you end up, that sounds as close as you can get to accurate, and you can still file, too.
BUT, please please please, keep records of everything and of all your attempts to rectify others' mistakes.
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