It's good (mostly) that you have two separate HSA accounts, because when one of you turns 55, you will be able to increase the annual HSA contribution limit for that person's HSA by $1,000 (but pro-rated the first year). The catch is that extra $1,000 has to go into that person's HSA.
No, having two separate HSA accounts does not affect this $1,200 excess. When you have Family HDHP coverage, the annual HSA contribution limit is shared by the two married taxpayers, in any way that you like (although TurboTax works it out for you).
So for now, just pretend that you have one virtual HSA, and the excess applies to one HSA or the other (your choice).
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