Is it possible to see through TTL USB cables or anything else the G and F code exchange between the PI and Arduino?
If you upgrade to FarmBot OS v6.0.1, you can enable send/receive firmware logging in the logs settings menu by clicking the gear icon on the Logs page.
SENT Firmware logs will show all G and F codes sent to the firmware in the logs, while enabling
RECEIVED will show all firmware responses. Additional information is available in the tooltips for the settings.