It comes down to the original artwork plus masking to create the invisible sections of the icon. What tends to happen with 'photo realistic' icons is that there are no clean edges, they fade to white to match an expected white background, and of course no matter how white pixels look, not-quite-white is not white.
We will look at the icons and masks again before final release but in the mean time, changing the system colours to give a lighter background for the menu and toolbar should make the icon bleed less distracting.