Windows detects no mouse clicks inside a small area of the screen
Solution 1:
If you minimize everything (so as to not accidentally close the wrong application) then click into the empty space and press alt + f4 it will close that invisible application that's running.
Solution 2:
The problem must've been caused by some sort of adware program, because I ran ADWCleaner and the problem was instantly resolved without the need for even a restart.