Since the last Yosemite update (and by extension, El Capitan), VLC doesn't go on a second desktop anymore when I press the fullscreen button on the upper left of the window as it used to do :/
Thank you for your help :-)
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Having the same weird issue here. What has proven to kind of work for me on El Cap is using the green fullscreen button on the top left corner first (creates basically a black desktop with VLC controls in it) and then CMD+F twice when in fullscreen VLC (puts the content inside and the controls on top). To get it back to windowed mode CMD+F, switch to another Desktop, back to fullscreen VLC and click the green fullscreen button again... A bit fiddly and certainly annoying. it seems like the VLC interface doesn't respect the way Mac OS handles fullscreen right now. Anyway, I hope that workaround works for you. You could still create a second desktop like the commenters before me suggested, would probably be easier.
Just go into Preferences, click the video tab and in the Fullscreen video device choose the screen you want VLC to be in.
@justsomerandomdude has provided the good answer to this problem. Quoting them:
I just found the fix to this. Basically you just have to go in to the settings and select "show all" in the bottom left, expand "Interface", expand "main interfaces", go into macosx and select "use native full screen mode" (or something along those lines, using different localization here).
Go to preferences, click on video tab and unselect the Black screens in Fullscreen mode. See this screenshot