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An ECS/Fargate tasks stops when the application in your container stops (or for that matter if a critical container exits for any reason). If your container doesn't shut down, the task will keep on running. It would be good to take a closer look and see if there are any additional processes that continue to run in this case.
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Thanks for this guess. Indeed in the middle of the entrypoint I launch some 3rd party software, which might be spawning process(es). I'll try to verify that and decrease stopTimeout of container to see if it helps.