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Check your printing tolerances or nozzle diameter. I made a hole adjusted for 10mm magnets with proper tolerance (10,2 and 10,5 wouldn't work by the way).

I wouldn't use hot glue with PLA. I recommend Loctite super glue or similar. Place a dab of glue in the cavity and press fit the magnet into it - it will lodge itself into the cavity and stay there. I don't recommend sanding the holes bigger if you haven't tried press fitting it yet.