#include<bits/stdc++.h>
using namespace std;
stack<char> S;
int main()
{
    ios_base::sync_with_stdio(0);
    cin.tie(0);
    cout.tie(0);
    string s;
    cin >> s;
    int len = s.length();
    for(int i = 0; i < len;i++)
    {
        char c;
        if(S.empty())
            c = 0;
        else
            c = S.top();
        if(c == s[i])
            S.pop();
        else
            S.push(c);
    }
    string ans = "";
    len = S.size();
    for(int i = 0; i < len;i++)
    {
        char c = S.top();
        ans += c;
        S.pop();
    }
    reverse(ans.begin(),ans.end());
    cout << ans;
}

You should do S.push(s[i]) in your else clause inside the for loop.