scanner not working properly inside if statement

You should use #equalsIgnoreCase

Use scan.nextLine().equalsIgnoreCase("y") instead, as || will go and check both the conditions as you will be prompted for nextLine() twice.

If you want user to keep asking for input if user enters wrong input you should use loop and prompt until condition gets satisfied.

For Example

     do {
         System.out.println("Type 'y' OR 'Y' to Exit!");
         if(s.nextLine().equalsIgnoreCase("y")) {
            customer.setBooked();
            break;
         }
      } while(true);

It is prompting twice, because you are asking it to prompt twice.

here : if (scan.nextLine().equals("y") || scan.nextLine().equals("Y")) You are calling scan.nextLine() two times.

Change your code to :

String s = scan.nextLine();
s=s.toLowerCase(); // change "Y" to "y" . Cleaner code.

if(s.equals("y")){
//your code here
}

Try using following code:

System.out.println(customer.isBooked());
System.out.println( "Confirm booking for " + customer.getName() + "(Y/N)");
Scanner scan = new Scanner(System.in);
boolean flag = scan.nextLine().equalsIgnoreCase("y");
if (flag)
    customer.setBooked();
System.out.println("Booked");
System.out.println(customer.isBooked());

You are calling scan.nextLine() twice in the condition, using an OR. This means that if the left side is not true, then it will continue to the right side. However if it is true, then the OR will be true and does not need to evaluate the right side. That is why if when they enter y the first time it only asks for it once, but otherwise it asks for it twice.

If you only want it to ask for it once, then instead of doing that assign the value of scan.nextLine() to a variable and use that variable in the if statement.

String result = scan.nextLine();
if (result.equals("y") || result.equals("Y")) {
    ...
}

Yes, You are calling two times

 scan.nextLine().equals("y") || scan.nextLine().equals("Y") //2 scan.nextLine()

Change your code to

 String line=scan.nextLine();
 if ("y".equals(line) ||"Y".equals(line)) // avoid NullPointerException too

Or use equalsIgnoreCase()

 if("y".equalsIgnoreCase(scan.nextLine())) // avoid NullPointerException too 

You are stating it should prompt twice here:

if (scan.nextLine().equals("y") || scan.nextLine().equals("Y"))

by calling scan.nextLine() twice.

What you could do is the following:

...
String next = scan.nextLine();    

if (next.equals("y") || next.equals("Y"))
...