Unexpected output when creating a List of Lists in Java

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You are adding all the integers to the same inner list (the one that you create at the start of your method with the statement List<Integer> l1 = new ArrayList<Integer>();).

You should create a new List before adding elements to it:

for(int i=1; i<n; i++) {
    if(S.charAt(i)==S.charAt(i-1)) {
        count++;
    } else {
        i2 = i-1;
        if(count>=3) {
            List<Integer> l1 = new ArrayList<Integer>();
            l1.add(i1);
            l1.add(i2);
            l2.add(l1);
        }

        count =1;
        i1=i;
    }
}

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