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There's a few design oddities at play here. How are you affixing the connections to the buttons? If you're using anything that resembles an OBSF-24 or OBSF-30, those will need solder jumpers with those giant holes. It's much better to just have smaller holes at exact positions on the board, where you can flow solder onto the connectors (to bridge them onto pads on the board). Have a look at the NeoFighter project to see what I'm on about. Also, the NeoFighter project is a great one to mirror both your LED choice and layout from. The SK6812 Mini LEDs are both small enough to fit around 24mm transparent buttons, and individually addressable. Also, it's far better to use two LEDs around each button, since your layout (and use of a single LED) would require extra light pipes (which would add unnecessary hassle and thickness). My only other advice is to look into some basic hardware debouncing, and to consider ESD protection (like a TVS diode) for your incoming USB connections. You can take a peek through my post history if you want to see some related schematic work (as I'm building a similar design to yours). Also, I highly recommend referencing existing Arduino schematic designs (if you hadn't already), as they make it far easier to handle some of the things that are really easy to overlook.