The reason you are entering more then 5 number is because the while loop will go until someone enters a number<1. Instead the while loop should check if numamount < 5. Then have an if statement check if the entered number<1.

public static void main(String[] args) {
// TODO code application logic here
//Create Scanner
Scanner input = new Scanner(System.in);
int number = 0, sum = 0, numamount = 0; // You can change the variable names.
while(numamount < 5)
{ // Begin while statement
System.out.println("Enter a number that is positive or zero: "); // Get the next number
number = input.nextInt();
if (number < 0){
System.out.println("you have Entered an invalid number, please enter again: ");
number = input.nextInt();
}
sum = sum+number; // Get the sum so far.
numamount++; // Get the number amount so far.
} // End while statement.
double average = sum/numamount; //Get the average.
System.out.println("You have entered " + numamount + " numbers"); // Output amount of numbers
System.out.println("Total of the numbers you entered is " + sum); // Output sum of numbers
System.out.println("Average of the numbers is " + average); // Output average of numbers.
}