resistor R12 (2M) and a few other components does not appear in file gerber

[hvuitsme]

I checked that the Top designator part doesn't show the 2M(R12) resistor and I can't fix it

[hvuitsme]

[zhiayang]

since I did not provide the BOM and pick-and-place file (BOM/CPL), I don't think I can help you here.

[hvuitsme]

I got the prototype in your repository
Bom file is still the same with this pos file

mikoto-top-pos.csv

[zhiayang]

how did you generate this file? some of the parts (like R12) are missing rotation values. that seems to be the problem.

[hvuitsme]

I choose to export that file according to the selected steps as shown in the picture

[cscott]

You should probably use the JLC Fabrication Toolkit plugin, available from KiCad's plug-in manager, to generate the production files.