Problem with circuit and led
I can see something strange:

your LEDs are connected between the MCU pins and the GND, without any resistors in series.
Thus the voltages at the pin will not exceed the Vf of your LED.

And this is a problem, because it's likely that you are overloading your MCU pins. You should patch your PCB and add a resistor in series with each LED.

By the way, on the schematics, there are resistors close to the LED, but it seems they are just connected between MCU pins and GND. Is it a mistake ?