VLC is still running even I closed it already. How to I close it?

Open "Run a command" window by pressing Alt+F2 or run the following from a terminal:

Try killall vlc to send SIGTERM to all instances of vlc (Tell em to terminate themselves).

If this does not work, try killall -s 9 vlc to send a SIGKILL (Tell the system to kill the processes).

I have resolved with this: https://learnubuntumate.weebly.com/vlc-closes-fix.html

1. Delete folder /home/your user/.config/vlc
2. open vlc
3. Open Preferences dialog, click on the Videos tab or button at the top. Then change your output to OpenGL video output.
4. Then click on the Input / Codecs tab or button at the top. Then change Hardware-accelerated decoding to Disable and then click the Save button. Now close VLC Media Player.

Works for me

As an addendum to forkirara's answer, it seems that setting Video Output to 'XVideo output (XCB)' also works (tested on Ubuntu 20.04 and PopOS 20.04). This also seems to bypass the need to delete the VLC config folder.

(Sorry for responding as an answer, Stack Exchange forces you to do so until you get the right to make addendums properly as comments).

Hope this helps anyone else coming here because VLC still hasn't fixed this bug!