I have experienced a LOT of glitches on both Safari on El Capitan and iOS 9, and with some apps using Webkit (UIWebView),
It was occurring mostly when a text, with RGBA color and opacity, was rendered inside an element that was doing a transition and linear gradient. And similar problem with PNGs with transparency that were compressed (probably reducing the amount of colors available).
What I found on interesting is that on both cases the transparency or the color of the element where changing to the "opposite" color of the scale ( transparent on blue -> dark red, orange -> blue ). In the example screenshot http://cl.ly/image/1c2Q2a0n2P38 the first column should be orange as the third one, and the third one should be totally in orange. I fixed that by removing the text out of the element in a new one with position absolute and bigger z-index.
As well the some FONTS with special elements (alpha, beta, gamma) are rendering "bolder" than on iOS 8 even if there is a CSS rule saying that. I am still investingating about this error.
I can't share the code or the entire screenshot for obvious reasons,
but I hope somebody will fix this ASAP since this is slowing down our deliveries and business.