A karakter és az int tipusú változók konverziója okozta a problémát.

#include <Keypad.h>
int BE=0;
int M=0;
int S=0;
const int A=2;
const int B=3;
const int C=4;
const int D=5;
const byte ROWS = 4;
const byte COLS = 3;
char key;
char keys[ROWS][COLS] = {
  {'1','2','3'},
  {'4','5','6'},
  {'7','8','9'},
  {'*','0','#'}
};
byte rowPins[ROWS] = {9, 8, 7, 6};   //számok felül és balról jobbra csatlakoztatva
byte colPins[COLS] = {12, 11, 10};

Keypad keypad = Keypad( makeKeymap(keys), rowPins, colPins, ROWS, COLS );
 
void setup() {
  pinMode(A, OUTPUT);
  pinMode(B, OUTPUT);
  pinMode(C, OUTPUT);
  pinMode(D, OUTPUT);
  Serial.begin(9600);
  }
 
void loop() {
  key = keypad.getKey();
  if (key != NO_KEY){
    BE=key;
    BE=BE-48;    
    M=BE-S;
    S=BE;
    to_BCD();
    }   
}

void to_BCD()
{
    if (BE == 0 ) //write 0000
    {
      digitalWrite(A, LOW);
      digitalWrite(B, LOW);
      digitalWrite(C, LOW);
      digitalWrite(D, LOW);
    }
     
    if (BE == 1 ) //write 0001
    {
      digitalWrite(A, HIGH);
      digitalWrite(B, LOW);
      digitalWrite(C, LOW);
      digitalWrite(D, LOW);
    }
     
    if (BE == 2 ) //write 0010
    {
      digitalWrite(A, LOW);
      digitalWrite(B, HIGH);
      digitalWrite(C, LOW);
      digitalWrite(D, LOW);
    }
     
    if (BE == 3 ) //write 0011
    {
      digitalWrite(A, HIGH);
      digitalWrite(B, HIGH);
      digitalWrite(C, LOW);
      digitalWrite(D, LOW);
    }
     
    if (BE == 4 ) //write 0100
    {
      digitalWrite(A, LOW);
      digitalWrite(B, LOW);
      digitalWrite(C, HIGH);
      digitalWrite(D, LOW);
    }
     
    if (BE == 5 ) //write 0101
    {
      digitalWrite(A, HIGH);
      digitalWrite(B, LOW);
      digitalWrite(C, HIGH);
      digitalWrite(D, LOW);
    }
     
    if (BE == 6 ) //write 0110
    {
      digitalWrite(A, LOW);
      digitalWrite(B, HIGH);
      digitalWrite(C, HIGH);
      digitalWrite(D, LOW);
    }
     
    if (BE ==7 ) //write 0111
    {
      digitalWrite(A, HIGH);
      digitalWrite(B, HIGH);
      digitalWrite(C, HIGH);
      digitalWrite(D, LOW);
    }
     
    if (BE == 8 ) //write 1000
    {
      digitalWrite(A, LOW);
      digitalWrite(B, LOW);
      digitalWrite(C, LOW);
      digitalWrite(D, HIGH);
    }
     
    if (BE == 9 ) //write 1001
    {
      digitalWrite(A, HIGH);
      digitalWrite(B, LOW);
      digitalWrite(C, LOW);
      digitalWrite(D, HIGH);
    }
}