If you use F.lux
F.lux has a known issue (see seventh bullet point) of display flickering on El Captian. You can fix it by turning off your Mac's
Automatically Adjust Brightness feature.
To turn off
Automatically Adjust Brightness, go to System Preferences -> Display.
If you don't use F.lux
Your issue sounds like a bug in OS X. It may be fixed in Sierra, but if you don't want to try out the beta first, you can easily stop it from happening by switching to F.lux:
- Delete the
Warm Colors profile (or any other display profiles you have set up in System Preferences -> Display -> Color)
- Download F.lux and follow the setup to get your ideal screen warmth (if you want your screen to turn warmer at night).
- Set up F.lux to turn on automatically at your desired time or just turn off that functionality and turn it on/off manually.