yes, not necessarily specific colors missing but whatever colors that are the same as the current bullet color. had this a couple times. unfortunately i haven't looked at a centipede in quite a while and I know longer have much of that section committed to memory, though there are only a few things that should cause this in the video drawing circuits.
I'm certain I have a few examples on my centipede repair page
http://www.arcade-cabinets.com/resources.shtml
give it a look and see if any of those help you. it's possible the missing shots/missing/eyes/missing sprite colors are written up on the millipede page (or both) don't recall, but I"ve seen that a couple times. I'm trying hard to remember /isolate it down to a few components to check but my memory is failing me at this time. sorry