Some times when asking jmeter to stop a running thread group a null pointer exception is thrown and the window saying "Stopping Threads" remains displayed.
The exception is:
Exception in thread "Thread-357" java.lang.NullPointerException
	at org.apache.jmeter.engine.StandardJMeterEngine.tellThreadsToStop(StandardJMeterEngine.java:542)
	at org.apache.jmeter.engine.StandardJMeterEngine.access$700(StandardJMeterEngine.java:57)
	at org.apache.jmeter.engine.StandardJMeterEngine$StopTest.run(StandardJMeterEngine.java:357)
	at java.lang.Thread.run(Unknown Source)

It seams a null check on the Thread object retreived should be done in this method:

    private void tellThreadsToStop() {
        synchronized (allThreads) { // Protect iterator
            Iterator<JMeterThread> iter = new HashSet<JMeterThread>(allThreads.keySet()).iterator();
            while (iter.hasNext()) {
                JMeterThread item = iter.next();
                item.stop(); // set stop flag
                item.interrupt(); // interrupt sampler if possible
                Thread t = allThreads.get(item);
                t.interrupt(); // also interrupt JVM thread           // <-- Line 542
            }
        }
    }

Regards,

Stephane