Program: 24431
Project: 24431
Buggy source:
@Override protected Void doInBackground(Void... params){
  List<Movie> movies=new ArrayList<Movie>();
  List<Track> videoTracks=new LinkedList<Track>();
  List<Track> audioTracks=new LinkedList<Track>();
  try {
    for (int i=0; i < videoFiles.size(); i++) {
      movies.add(MovieCreator.build(videoFiles.get(i).getAbsolutePath()));
    }
    for (    Movie m : movies) {
      for (      Track t : m.getTracks()) {
        if (t.getHandler().equals("String_Node_Str")) {
          audioTracks.add(t);
        }
        if (t.getHandler().equals("String_Node_Str")) {
          videoTracks.add(t);
        }
      }
    }
    Movie finalMovie=new Movie();
    if (audioTracks.size() > 0) {
      finalMovie.addTrack(new AppendTrack(audioTracks.toArray(new Track[audioTracks.size()])));
    }
    if (videoTracks.size() > 0) {
      finalMovie.addTrack(new AppendTrack(videoTracks.toArray(new Track[videoTracks.size()])));
    }
    Container out=new DefaultMp4Builder().build(finalMovie);
    FileChannel fc=new RandomAccessFile(finalVideoFile,"String_Node_Str").getChannel();
    for (int i=0; i < out.getBoxes().size(); i++) {
      finalVideoFileSize+=out.getBoxes().get(i).getSize();
    }
    Thread t=new Thread(new Runnable(){
      @Override public void run(){
        Log.e("String_Node_Str","String_Node_Str");
        long currentFileSize=0;
        if (finalVideoFile.exists())         currentFileSize=finalVideoFile.length();
        while (finalVideoFileSize != currentFileSize) {
          try {
            Thread.sleep(5000);
          }
 catch (          InterruptedException e) {
            e.printStackTrace();
          }
          if (finalVideoFile.exists()) {
            currentFileSize=finalVideoFile.length();
            Log.e("String_Node_Str","String_Node_Str" + finalVideoFileSize + "String_Node_Str"+ currentFileSize);
            int progress=(int)(currentFileSize * 100 / finalVideoFileSize);
            publishProgress(progress);
          }
        }
        Log.e("String_Node_Str","String_Node_Str");
      }
    }
);
    t.start();
    out.writeContainer(fc);
    t.stop();
    fc.close();
    for (int i=0; i < videoFiles.size(); i++) {
      videoFiles.get(i).delete();
    }
    publishProgress(100);
  }
 catch (  Exception e) {
    exception=e;
  }
  return null;
}

Fixed version (ground truth):
@Override protected Void doInBackground(Void... params){
  List<Movie> movies=new ArrayList<Movie>();
  List<Track> videoTracks=new LinkedList<Track>();
  List<Track> audioTracks=new LinkedList<Track>();
  try {
    for (int i=0; i < videoFiles.size(); i++) {
      movies.add(MovieCreator.build(videoFiles.get(i).getAbsolutePath()));
    }
    for (    Movie m : movies) {
      for (      Track t : m.getTracks()) {
        if (t.getHandler().equals("String_Node_Str")) {
          audioTracks.add(t);
        }
        if (t.getHandler().equals("String_Node_Str")) {
          videoTracks.add(t);
        }
      }
    }
    Movie finalMovie=new Movie();
    if (audioTracks.size() > 0) {
      finalMovie.addTrack(new AppendTrack(audioTracks.toArray(new Track[audioTracks.size()])));
    }
    if (videoTracks.size() > 0) {
      finalMovie.addTrack(new AppendTrack(videoTracks.toArray(new Track[videoTracks.size()])));
    }
    Container out=new DefaultMp4Builder().build(finalMovie);
    FileChannel fc=new RandomAccessFile(finalVideoFile,"String_Node_Str").getChannel();
    for (int i=0; i < out.getBoxes().size(); i++) {
      finalVideoFileSize+=out.getBoxes().get(i).getSize();
    }
    Thread t=new Thread(new Runnable(){
      @Override public void run(){
        fileSizeCheckerThread=true;
        Log.e("String_Node_Str","String_Node_Str");
        long currentFileSize=0;
        if (finalVideoFile.exists())         currentFileSize=finalVideoFile.length();
        while (currentFileSize < finalVideoFileSize) {
          try {
            Thread.sleep(5000);
          }
 catch (          InterruptedException e) {
            e.printStackTrace();
          }
          if (finalVideoFile.exists()) {
            currentFileSize=finalVideoFile.length();
            Log.e("String_Node_Str","String_Node_Str" + finalVideoFileSize + "String_Node_Str"+ currentFileSize);
            int progress=(int)(currentFileSize * 100 / finalVideoFileSize);
            publishProgress(progress);
          }
          if (currentFileSize >= finalVideoFileSize)           break;
        }
        fileSizeCheckerThread=false;
        Log.e("String_Node_Str","String_Node_Str");
      }
    }
);
    t.start();
    out.writeContainer(fc);
    fc.close();
    for (int i=0; i < videoFiles.size(); i++) {
      videoFiles.get(i).delete();
    }
    publishProgress(100);
    if (fileSizeCheckerThread)     Thread.sleep(5000);
  }
 catch (  Exception e) {
    exception=e;
  }
  return null;
}