What I have noticed is that if you just open a plugin window in Bitwig 3.1, and you don't move it around, then you can close it with the x symbol.
But if you move the plugin on the screen, then the x won't work instantly, you'd have to click the x and then start dragging the plugin to make it disappear.
Unfortunately I don't have any plugins from other developers on the Linux VM, so I can't determine if this happens only with our plugins, or if this is a general Bitwig issue.