Weird El Capitan interface / icon glitch - clear cache?
Not sure this is going to fix it since I haven't experienced it myself yet, but I had issues in the past on older versions of OSX where some toolbar icons would get garbled and booting into safe mode would fix it.

Though documented on this Apple support page, the short of it is that you need to reboot and hold down the shift key after the startup sound plays (release after the Apple logo appears). The computer will boot and run much slower, but it is doing a bunch of housekeeping in the process. Let it complete loading and log in to your desktop and then at some point you can reboot again (no shift this time) and hopefully things are back to normal.