On my laptop running Ubuntu 16.04, the mouse pointer disappeared frequently.
My problem was: The mouse pointer seemed to disappear when I moved to the right side of the screen. It then appeared after say 3 to 5 seconds after moving the mouse up, down, left, right. This was quite annoying when doing work on the computer.
The solution was:
Click Dash (upper left corner) and type "system settings".
Click "System Settings", then All Settings > Displays
If its as of my case, you will see a box call Unknown Display to the left of Built in Display in a big box with grey background
Click on unknown display and de-activate it by turning off the button just below the grey box.
I found the answer here (Thanks to Justin Samuel!).