I ran into this issue with my Samsung Note 4. In my case it was the Side key panel which was causing this problem. I turned it off and the problem went away.
Settings -> Display and Wallpaper -> One-handed operation. Uncheck Side key panel.
If this doesn’t apply to you or doesn’t solve the issue, please check other apps that have ‘Draw over other apps’ or ‘Apps that can appear on top’ setting enabled. Try disabling the setting for each app and see if it resolves the issue. The usual suspects are Clean Master, Twilight, File Manager, any battery saving app among others.
De-install from clean master was the solution for a Acer liquid 4G to get rid of the above problem… After the problem was gone I did not try to install clean master again…