When attempting to stop a parent job in Spoon, child jobs and transformations do not stop and will continue to run.
Steps to recreate:
1) Create a parent job and a child transformation or job
2) Run parent job and hit the stop button
3) Open up child transformation or job and view the step metrics, you'll see they continue to run.
The only way to stop the child elements is to open them up outside of the parent job and stop them, please review screencast for an example of the behavior: