Yeah, hitting exactly where you want in a side panel with a biscuit jointer isn’t that easy. When my slots are slightly off, I hit em again with the jointer. A slightly wide slot is better than no biscuit, IMHO.
I’d adjust the slots that need adjusting by removing some more material. If I had only a drill and a utility knife, I would do a bit of careful drilling and clear out the chunks with the knife.
Biscuit jointers are great with 3/4” materials and thicker. For our 1/2” Baltic birch, (12mm) it takes some adjusting with a jig to get the biscuit centered in the thickness of the panel. And it’s really easy to get a little off doing the cut into the side for the baffle biscuits.
Once you’ve adjusted the baffle biscuits, and everything fits, drill a few pilot holes and use small screws to hold things.
Double check to make sure the baffle is oriented correctly and facing the right way.
For a real brain twister, try a 12/6 cube from scratch.
Don’t forget to reward yourself when you get it together. These are the cheap harbor freight clamps. If one ever slips, they’ll give me another. Notice all the marks.
Nice job sussing out the issue. Carpentry is all about really seeing what’s going on. Keep on keeping on!