Digital pin always outputs current during deep sleep

During deep sleep, I think the output from the microcomputer board is disabled.I don't know which digital pin you're using, but if you're using an expansion board pin, it's pulled up to 3.3V or 5V via a level shifter on the board, so that's probably the reason.

I'm going to repeat the answer, but I'd like to explain it a little more clearly.

As kzz pointed out, there is always a voltage on the expansion board pins.If you don't control anything on the main board, the current will flow if you apply an LED-like load.

(In other words, the expansion board can flash LEDs because the main board controls the pins to do so.)

This is a little difficult to understand, so I removed the main board and tested to see if the LED would glow only on the expansion board.As you can see, the LED is shining only on the expansion board.

(The USB power supply on the main board and the USB power supply on the expansion board are the same.)

On the other hand, I connected the LED to the main board and repeatedly started DeepSleep.As you can see, there is no current in GPIO during DeepSleep.

The sketches I used are as follows:

#include<LowPower.h>
#define LED_PIN0

void setup() {
  pinMode (LED_PIN, OUTPUT);
  digitalWrite (LED_PIN, HIGH);
  delay (2000);
  LowPower.begin();
  LowPower.deepSleep(2);
}

void loop() {
}

As a result, the main board must be loaded to reduce power consumption during DeepSleep.

I hope it will be helpful.

Let's check the schematic first.
Generally, the GPIO port is asleep and open, but the circuit connected to it may be open and current flows.
Also, some ports have specific output during sleep, so you need to read the CPU datasheet to see how the pins work