This kind of thing would also be my next guess. It would certainly also be nicer if it were a software problem of some kind rather than an electronics one.
But since you’re taking in values via modbus from an external source, its good practice anyway to check them. I don’t know modbus, so perhaps the library has already solved it for you, but if not then I would definately put in a check to see if the values are in the expected range and make sense in the context of the current program state.
If you have an unexpected value, you could use the LED to indicate it.
I assume you checked it? Because most STM32s have several serial peripherals and several UART pins… Do you program via SWD? The SWO pin (if available) would be another way to get debug output.
Otherwise, getting some telemetry via modbus might be a good idea. If not, its down to the LED 