Those label good to have but I think it may create some vibrations, try use masking tape to secure it down with the cables to see it improve. Next build, you may want to have more holes or groove on carbon fiber plate for tying down cables and running cables to different level. Yes, you have cable tie the extra cables length but they appear “floating” to me and not secure to plate to prevent movement. Do you think those cables below the flight controller are knocking the top plate?
How do you secure the Flight controller to the plate? Screw from bottom? Double-sided tape?
Do you think the drone arm joint can flex up or down if you use some force trying to bend it?
You can try cover up the flight controller for a few benefits. Reduce propeller wash vibration, barometer drastic changes especially pitch and roll, etc.
Is this part movable? If yes, try masking tape it down to the arm to prevent from moving to see if it is the cause.