The immediate problem is due to you using <= temp.length() instead of < temp.length(). However, you can achieve this a lot more simply. Even if you use the string approach, you can use:

String temp = Integer.toString(guess);
int[] newGuess = new int[temp.length()];
for (int i = 0; i < temp.length(); i++)
{
    newGuess[i] = temp.charAt(i) - '0';
}

You need to make the same change to use < newGuess.length() when printing out the content too - otherwise for an array of length 4 (which has valid indexes 0, 1, 2, 3) you'll try to use newGuess[4]. The vast majority of for loops I write use < in the condition, rather than <=.

You can convert entire string and then you get the toCharArray method separately characters in an array

Scanner t = new Scanner(System.in);
     int x = t.nextInt();
     char[] xd = String.valueOf(x).toCharArray();

    for (int i = 0; i < xd.length; i++) {
        System.out.println(xd[i]);
    }

Another way of doing this would be:

int test = 12345;
        int[] testArray = new int[String.valueOf(test).length()];

And then looping over it.