io - Java Scanner doesn't wait for user input

It's possible that you are calling a method like nextInt() before. Thus a program like this:

Scanner scanner = new Scanner(System.in);

int pos = scanner.nextInt();
System.out.print("X: ");
String x = scanner.nextLine();
System.out.print("Y: ");
String y = scanner.nextLine();

demonstatres the behavior you're seeing.

The problem is that nextInt() does not consume the '\n', so the next call to nextLine() consumes it and then it's waiting to read the input for y.

You need to consume the '\n' before calling nextLine().

System.out.print("X: ");
scanner.nextLine(); //throw away the \n not consumed by nextInt()
x = scanner.nextLine();
System.out.print("Y: ");
y = scanner.nextLine();

(actually a better way would be to call directly nextLine() after nextInt()).