"penalty for what though?"

Right here:

"and 5329-S"

S = spouse

You would have to confirm, since the Spouse has contributed, if that is too much per the type of policy each spouse has. In other words, it's a matrix of one Family coverage that doesn't cover the Spouse, and one spouse has Self-only coverage? Or, they both have Family coverage? Or maybe the one spouse is not covered under HDHP, for self?

Because that matrix drives how much they can contribute to each HSA or to the one HSA account, per the HDHP coverage.