My kid had almost the exact same situation. The admissions portals don’t always have good info, but you can see what the schools downloaded if you go to common app.
Go to the My Colleges tab, pick the school, and go to the Reccomenders and FERPA tab on on the sidebar.
My son got lucky that the 1 letter he preferred was the one that got submitted 1st, but he was able to confirm what the schools downloaded by looking here. If you want, you can address it with any school that has downloaded only the one you don’t want. But I agree with others that it’s likely not a big deal.
Here is what it looked like for a school that downloaded 2 vs a school that only downloaded 1. But maybe you already did this, not sure. Perhaps it can help someone else.
Edited to add: I just went and looked at naviance for the first time since he submitted his common app. His GC had originally sent 2 letters to every school, and that’s how it showed up in Naviance at the time of applying. Now it’s only showing that the 2 letters were sent to some of the schools. I’m not sure if my son asked her to change it after the fact or what happened. But it definitely changed.