How to Perform Fragment Transactions to avoid Activity.onSaveInstanceState Error

MainActivity.java

import android.content.Context;
import android.support.v4.app.Fragment;
import android.support.v4.app.FragmentTransaction;
import android.support.v7.app.AppCompatActivity;
import android.os.Bundle;

import java.util.ArrayDeque;
import java.util.Queue;

public class MainActivity extends AppCompatActivity {

    private boolean isRunning;
    private Queue<FragmentTransaction> mFragmentTransactions = new ArrayDeque<>();

    @Override
    protected void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
        setContentView(R.layout.activity_main);

        setupBaseFragment();
    }

    @Override
    protected void onPostResume() {
        super.onPostResume();
        isRunning = true;

        if(mFragmentTransactions != null)
            while(!mFragmentTransactions.isEmpty())
                mFragmentTransactions.remove().commit();
    }

    @Override
    protected void onStop() {
        isRunning = false;
        super.onStop();
    }

    public void setupBaseFragment(){
        //Find Active Fragment if Available
        Fragment baseFragment = getSupportFragmentManager().findFragmentById(R.id.fragment_container);

        //Create Fragment if no Fragment is Available
        if(baseFragment == null)
            baseFragment = new HomeFragment();

        setFragment(baseFragment, false);
    }

    public void setFragment(Fragment fragment, boolean addToBackStack){
        if(fragment == null)
            return;

        //Create New Transaction
        FragmentTransaction ft = getSupportFragmentManager().beginTransaction();

        ft.replace(R.id.fragment_container, fragment, fragment.getClass().getCanonicalName());

        if(addToBackStack)
            ft.addToBackStack(fragment.getClass().getCanonicalName());

        //Commit Transaction if Activity is running else wait for Activity to Resume
        if(isRunning){
            ft.commit();
        } else {
            mFragmentTransactions.add(ft);
        }
    }

    public void addFragmentOnTop(Fragment fragment, boolean addToBackStack){
        if(fragment == null)
            return;

        //Create New Transaction
        FragmentTransaction ft  = getSupportFragmentManager().beginTransaction();

        ft.add(R.id.fragment_container, fragment, fragment.getClass().getCanonicalName());

        if(addToBackStack)
            ft.addToBackStack(fragment.getClass().getCanonicalName());

        //Commit Transaction if Activity is running else wait for Activity to Resume
        if(isRunning){
            ft.commit();
        } else {
            mFragmentTransactions.add(ft);
        }
    }

    public Fragment getFragment(String fragmentTag){
        return getSupportFragmentManager().findFragmentByTag(fragmentTag);
    }
}