The outside diameter of the brake rotor rubs against the caliper
You're not missing anything. Sometimes this just happens.
There is a bigger question at hand regarding what aspects of the relevant parts dimensions are truly standardized, and which are the kind of informal follow-the-leader standards the bike industry often uses. It doesn't really matter and I couldn't write that answer.
Use up to 2mm or so of shim/washer on each bolt. Normal M6 washers are fine, or you could use fancy ground ones if you have them. Make sure the bolts keep at least 6mm of thread engagement and use longer bolts if not. Other than that, all you care about is the pad contact on the rotor. You are shooting for no overhang of the pad, such that the entire pad face is contacting with no potential for a lip to build up as the pad wears.