This is a minor GUI glitch that may also be OS-specific: sometimes the small windows containing function syntax information that pop up while typing a command get stuck. Right now I'm using R2016a on linux Mint 18, but it also happens in several older matlab distributions and Ubuntu/Mint linux versions.
When such a window gets stuck it blocks whatever happens to be behind it on the main GUI window until I restart the GUI. This usually means that whatever text I may be typing on the command line will be obstructed -- which is annoying. However, the stuck pop up stays put when I resize or move the GUI window around, which is how I deal with this now. The pop-up also doesn't obstruct other windows, including other matlab windows (e.g. the editor or help windows), or other applications I may be running. Which is why it's just a minor annoyance.
Is there any way to clear these stuck pop-ups without killing the entire session? These things don't fail often enough to disable them entirely, but having to restart the GUI just to clear them is obnoxious.