Jupyter notebook server does not quit

[stumbrok]

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When trying to quit the notebook by pressing on the button on frontend, server does not shutdown entirely. jupyter notebook list does not list any running server, jupyter notebook stop says that "There are no running servers", but when I check processes, the notebook process is still running. This does not occur always, but it happens in 1/5.

Notebook is running on ubuntu 18.04 in docker container(yes we do run it with --init flag).

Version:

jupyter core     : 4.6.3
jupyter-notebook : 6.0.3
qtconsole        : 4.7.2
ipython          : 7.13.0
ipykernel        : 5.2.0
jupyter client   : 6.1.2
jupyter lab      : not installed
nbconvert        : 5.6.1
ipywidgets       : 7.5.1
nbformat         : 5.0.5
traitlets        : 4.3.3

Notebook logs on quit:

[I 12:48:17.214 NotebookApp] Saving file at /Untitled.ipynb
[I 12:50:35.069 NotebookApp] Shutting down on /api/shutdown request.
[I 12:50:35.070 NotebookApp] Shutting down 1 kernel
{'content': {'restart': False},
 'header': {'date': datetime.datetime(2020, 4, 3, 12, 50, 35, 70961, tzinfo=datetime.timezone.utc),
            'msg_id': 'd1176e16-0524f2cd7579c1eb03d8001e_0',
            'msg_type': 'shutdown_request',
            'session': 'd1176e16-0524f2cd7579c1eb03d8001e',
            'username': 'username',
            'version': '5.3'},
 'metadata': {},
 'msg_id': 'd1176e16-0524f2cd7579c1eb03d8001e_0',
 'msg_type': 'shutdown_request',
 'parent_header': {}}
[b'<IDS|MSG>',
 b'95c556e63d83cd58709854ab75010a1ab67c0c2fd3465b3e145e1da121bb8f5f',
 b'{"msg_id":"d1176e16-0524f2cd7579c1eb03d8001e_0","msg_type":"shutdown_request'
 b'","username":"username","session":"d1176e16-0524f2cd7579c1eb03d8001e","date"'
 b':"2020-04-03T12:50:35.070961Z","version":"5.3"}',
 b'{}',
 b'{}',
 b'{"restart":false}']
[]
[I 12:50:35.372 NotebookApp] Kernel shutdown: 5c1bea7b-cfb6-4c63-8df6-9bdf76380fb2