Return the repeated number and the missing number
There is a shortcut you can take to find the missing number after you've found the duplicated number.  You may have come across this fact before, where the sum of the numbers 1 to n is n*(n+1)/2.  We can leverage this along with the duplicated number to find the missing number.  If you add up every number in your list and subtract that from what the expected sum would be from 1 to n, most of the terms will cancel, leaving you with missing - duplicate.  You can visualize that with an example:

 (1+2+3+4+5+6+7)
-(1+2+3+4+5+1+7)
=(6)-(1)


In that example, n is 7, the duplicated number is 1, and the missing number is 6.  So you get the formula expected_sum - actual_sum = missing - duplicate.  We can solve for missing by adding duplicate to both sides, leaving us with missing = expected_sum - actual_sum + duplicate!  Let's do that.

First, you can calculate the expected sum from that formula, n*(n+1)/2.  In your loop searching for the duplicate, you will need to keep a running total (and don't break early).  After you find the sum of your list and identify the duplicate number, you can calculate the missing number using the formula we talked about in the above example, missing = expected_sum - actual_sum + duplicate.

Also, you don't need to record the frequency as an integer, you can just keep a list of booleans for numbers already seen.  I've also taken the liberty of cleaning up the indentation issues and renaming some of the variables for the purpose of readability.  Here is the solution:

public class Solution {
    // DO NOT MODIFY THE LIST. IT IS READ ONLY
    public ArrayList&lt;Integer&gt; repeatedNumber(final List&lt;Integer&gt; A) {
        //O(n) solution
        //Keep a record of all the numbers appearing in the list        
        boolean [] seen = new boolean[A.size()];

        int rep_num = 0, miss_num = 0;
        int expected_sum = A.size() * (A.size() + 1) / 2;
        int actual_sum = 0;

        //Find sum of list and identify duplicate number
        for( int i = 0; i &lt; A.size(); i++ )
        {
            int num = A.get(i);
            if(seen[num - 1])
                rep_num = num;

            seen[num - 1] = true;
            actual_sum += num;
        }

        miss_num = expected_sum - actual_sum + rep_num;

        ArrayList&lt;Integer&gt; results = new ArrayList&lt;Integer&gt;();
        results.add(rep_num);
        results.add(miss_num);

        return results;
    }
}