Ooh, that's awkward. So the two choir teachers are definitely invited, because they're singing a duet. The daughter is coming because she's going to accompany them on the harp. That all makes sense to me.
But, it really should have stopped there. The son should never have been given the impression that he's invited.
Also, I don't think the daughter's boyfriend needs to be invited, even though they are a social unit. To me, this isn't really a "social" occasion, it's more like a work occasion. She is working at your wedding.
One thing you could do is call the parents and be like, "Oh, I'm so sorry, there's been some kind of mix-up. The venue is very small, so I won't be able to invite anyone from your family beyond you two, and Harpist. I hope this is okay." Then it will be on the parents, or whoever, to tell Son, daughter's boyfriend, etc. that they will not be getting in the car for the drive to your wedding.
If you were having just one musician who was performing with a tape, I think it would be kind to also invite their partner. More in the vein of "someone they know to travel and sit with" than anything else. But in this case it's two spouses and their daughter, who make up the musician package--that is plenty of people to travel and sit with.
But, if you're okay with/have agreed to some of the extra people coming (anyone beyond parents and one daughter), I'm kind of torn. Because on the one hand, you could call the parents and ask who they're planning to bring, who is "the whole family" that Son mentioned, and just make room for those people, whoever they are, and not suggest anyone else (like partners). Because you aren't really inviting them, you're just getting a list of people who invited themselves (or were invited by someone without authority to do so).
But on the other hand, I kind of feel like, if you're accepting that these extra people are coming, even though you didn't invite them, then the gracious thing to do is to treat them like full guests, with partners invited as you would if they'd been on your guest list from the beginning. Which in this case would certainly include Son's partner, since you know and like him, and also daughter's partner since at that point almost everyone in the family is invited EXCEPT him, which is awkward. And you wouldn't want your guests to feel awkward.