@mel mendoza
The execute stream command processor is still running on the own Flow File and is allowing the last thread to complete before releasing the thread i.e one thread is running on the flow file to execute the script/command and another thread is stopping the thread. In this NiFi processor state will no longer schedule to run, but it does not interrupt any running threads as you can see there is small 2 number in the upper right corner indicates the active number of threads.
This situation will happens when the processor is not configured properly (or) you need to look into your script that is running in execute stream command processor that causing this situation,To find out where the processor is hung then run several nifi.sh dump to figure out where exactly the processor hung
bin/nifi.sh dump thread-dump.txt
If the processor doesn't release the thread with in few minutes, you will have to Restart NiFi to force it to release the thread, as of now there is no force kill kind of operation in NiFi that can kill all the hanging threads.
Do NiFi restart then all the threads running on the processor will be released then you can clear the queue.
