First, there is no such thing as a joint HSA. The HSA is like an IRA in that it is owned by the individual. I know it seems like a joint account because both of you can use it, but in the eyes of the IRS, it is not.
Now, which issue are you referring to: the lapse in coverage or the HSA contribution not being deducted? These two issues are unrelated to each other.
Did you look at Preview my 1040? Is the deduction on line 12?
[Edited 3/16/2020 11:36 am CDT - typo]
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