One of my all-time favourite apps is f.lux, which reduces the blue harshness of a Mac/iPad/iPhone screen at night by altering the color temperature of the screen. It has been consistently useful enough for me (and missed sorely when absent!) to jailbreak an entire iOS device just to install it.
So I got really pissed off when my screen started having weird brightness fluctuations. At first I didn’t notice it much, and then I had a FaceTime call with a relative when the lighting was changing as I moved around, and it was horrible. Flashy flashy intermittent flashy AUUUGHH!
The problem is apparently that Apple’s auto screen brightness feature in El Capitan directly conflicts with f.lux’s. As a f.lux dev said here, the only fix is to disable Apple’s controller, so that it doesn’t fight with f.lux’s, producing a hot visual mess.
The problem can be resolved by going to System Preferences -> Display -> and unchecking “automatically adjust brightness” checkbox.