When you select the windowed option you should also set the Resolution to something smaller than your screen before pressing apply so that that doesn't happen.
You can still move the cursor around with the keyboard to reach the apply button, but if that doesn't work, maybe you can try delete the options file and restarting the game. The options file is at "C:\Users\<username>\AppData\Roaming\Labyrinth of Legendary Loot\options"