So, when I start watching a video or something of the like, VLC puts a nice little icon in the tray. The problem is, that when I open and close VLC it keeps adding another nice little icon in the tray.
Here's a SS for example's sake.
Go to Tools->Preferences
Check the option of “allow only one instance". You may want to check the related "Enqueue files in playlist when in one instance mode" too. Press save.