Why my Arduino pins are constantly giving out 2.9V ?

I am doing an Autocar project for my university robotic club challenge. The car have to autonomously follow black line and also have a programmable push buttons which can control programmable led. The shield is provided with 7.4V power source which is regulated to 5V and the motor is provided with a different 7.4V power source unregulated. The problem that I am having now is that when I turned on the shield which is attached to the Arduino, the Arduino is constantly giving out 2.9V from all of it's pin and thus making the programmable LEDs to light up. Why does this happen? Here is the schematic of my circuit (1st page is the main shield and the 2nd page is the sensor board). The blue colored notation is the potential different that I measured using multimeter from the pin to the ground before I push the programmable push button while the red notation is after I push the button. Here is the code that I wrote only for testing purpose.

//Motor 1
const int motor1Pin1 = 7;
const int motor1Pin2 = 6;
const int motor1PWM = 3;
//Motor 2
const int motor2Pin1 = 2;
const int motor2Pin2 = 4;
const int motor2PWM = 5;

//Programmable LED
const int ledPin1 = 9;
const int ledPin2 = 11;
const int ledPin3 = 13;

//Programmable Push Button
const int buttonPin1 = 8;
const int buttonPin2 = 10;

int pushButton1 = 0;
int pushButton2 = 0;
int Switch = 0;

int Value1;
int Value2;
int Value3;
int Value4;

void setup(){

//Set pins as outputs
pinMode(motor1Pin1, OUTPUT);
pinMode(motor1Pin2, OUTPUT);
pinMode(motor1PWM, OUTPUT);
pinMode(motor2Pin1, OUTPUT);
pinMode(motor2Pin2, OUTPUT);
pinMode(motor2PWM, OUTPUT);
pinMode(ledPin1, OUTPUT);
pinMode(ledPin2, OUTPUT);
pinMode(ledPin3, OUTPUT);
pinMode(buttonPin1, INPUT_PULLUP);
pinMode(buttonPin2, INPUT_PULLUP);
pinMode(A0, INPUT);
pinMode(A1, INPUT);
pinMode(A2, INPUT);
pinMode(A3, INPUT);

}

void loop(){

pushButton1 = digitalRead(buttonPin1);

if(pushButton1 == LOW){
digitalWrite(ledPin1, HIGH);
digitalWrite(ledPin2, HIGH);
digitalWrite(ledPin3, HIGH);
}
}