I just ran into this in beta 1.0.21844 and found it does it in MAS.
I have two shapes in my drawing. If I drag the one layer onto another to clip it, then drag it off to unclip it the icon in the layer panel looses its color. It's only shown white on black even though the actual image retains the correct color. If I change the color of the shape then the layer icon corrects itself.
Yosemite 27" iMac late 2009