Not sure about colour overlaps, or grey lines. I’ve not experienced them, but often very fine white lines on pdf/x files can be nothing to worry about and won’t show up when output. They are areas where the pdf has sliced images up. You can tell if they are part of the image (and are a problem) or part of the pdf structure (and not a problem), by zooming in on one of them to where you can see the pixels of the image. If they are a problem, these white lines will increase along with the pixels. If they are not, no matter how close you zoom in, those white lines don’t increase in size, ie remain thinner than the pixels you are seeing.
Anyway, this is off piste from the OP, but hope it helps.