This issue is very similar to this question, except it happens with the built-in trackpad.
After some time using the computer, the cursor stops tracking until I click. Interestingly, multi-touch works, all 2+ finger gestures work, including two-finger scrolling.
To clarify: the visible representation of the cursor (the arrow) does indeed move, but no application appears to notice that it has moved until I click. This means, for example, if I click a menu at the top and then move the cursor to another menu, the menu I'm now pointing at doesn't open. It also means that I cannot effectively use select/combo boxes without using the keyboard, as clicking opens the box, but then the mouse stops tracking again so I can't select an item. If I release the mouse, the select box simply closes with no change in selection.
The same issue happens with dragging desktop icons, or anything else around. I simply can't. Likewise, moving the cursor to the bottom of the screen will not cause the dock to appear. I cannot select text with the touchpad.
Logging out and back in to my account does fix the problem temporarily, however I'm very much over having to do this several times per day. Nevertheless, this at least illustrates that it's likely a software issue and not (necessarily) hardware.
This issue does not appear to affect external mice, only the touchpad. Plugging and unplugging an external mouse does not fix the touchpad.
It's a MacBook Pro running OS X 10.11.1. I had this same issue with 10.10.