To reproduce:

• make application like this:

  #include <QApplication>
  int main(int argc, char **argv)
  {
      QApplication app(argc, argv);
      qDebug("line 1");
      qDebug("line 2");
      return app.exec();
  }
  

• run it and it prints 2 lines
• kill it
• set filter in the Application Output to "line"
• run it

It only shows "line 1" in the output. Line 2 becomes visible once something more matching the filter is printed or when the application is killed.