I think it may be a bug. It seems to be a combination of the viewports angle and color difference. The pixels in question seem to have similar color difference compared to the surrounding pixels. While this seems to be a factor, the pixels that don’t get painted over is largely dependent on the view of the object in 3D viewport. Even zooming in and out result in different pixels. Go back to previous view it results in the same pixels everytime. I think this is a rare bug.
So, quick solution is to fill. zoom out a little. Fill again. So far 3 zoom outs has been the most I’ve had to do. Also orbit or pan the view a little helps to.
