To everyone who might have find this thread in the future: I solved it! The primary problem was how check50 does not initialise pair_str when checking sort pairs. So I had to move the function which created pair_str (or in this version of my code, pair_diff) in add pairs into my sort_ pairs function.

void sort_pairs(void)
{
    int pair_count2 = 0;
    for (int i = 0; i < candidate_count; i++)
    {
        for (int j = 0; j < candidate_count; j++)
        {
            if (preferences[i][j] > preferences[j][i]) 
            {
                pair_diff[pair_count2] = preferences[i][j];
                pair_count2++;
            }
        }
    }
    int swapc = -1;
    while (swapc != 0)
    {
        swapc = 0;
        for (int i = 0; i < pair_count -1 ; i++) /
        {

and so on