I booted my MacBook Pro a few days ago and some of the icons on my dock were not visible. I noticed that there were icons missing in Safari, Finder and Mail. I attach a screen-shot to make my issue more clear.
Try Safe Booting once. It causes all caches(including icon caches) to be rebuilt.
Steps for Safe Boot here
Choose Apple menu > Shut Down.
After your Mac shuts down, wait 10 seconds, then press the power button.
Immediately after you hear the startup tone, hold down the Shift key.
You should press the Shift key as soon as possible after you hear the startup tone, but not before.
Release the Shift key when you see the gray Apple logo and progress indicator.
To leave safe mode, restart your Mac again, but don’t hold down any keys during startup.