I am entering HSA contributions for a couple, both have a plan and I'm getting an error message for excess when they aren't over the limit.

Your first mistake is trying to decode what the Form 8889 instructions are telling you. They start out with:

“How To Complete Part I
“Complete lines 1 through 13 as instructed on the form. However, if you, and your spouse if filing jointly, are both eligible individuals and either of you has an HDHP with family coverage, you both are treated as having only the family coverage plan. Disregard any plans with self-only coverage.”

And then they go on to say the following. But does this next paragraph apply to the situation in the prior one, involving one spouse with family and the other with self-only? Or have we solved that problem, by disregarding the husband’s plan? Does that mean we have to disregard his contributions also?

“Complete a separate Form 8889 for each spouse. Combine the amounts on line 13 of both Forms 8889 and enter this amount on Schedule 1 (Form 1040 or 1040-SR), line 12; or Form 1040-NR, line 25. Be sure to attach both Forms 8889 to your paper tax return.”

The message I get is that IRS can’t deal with this either, so they want a paper return when both spouses have an HSA.

Are these contributions being made with after-tax dollars? When I see employer HSA’s, it’s usually through a cafeteria plan where the deduction is already taken on the W-2. But you still have to file the form. Unless it’s not required.