Just looks like dirt got on them to me. And yes, infertile eggs will still grow. Some can stay good all the way up to 6+ weeks, but still candle yellow/infertile.
It almost looks like the brown moss substrate that is attached to the eggs are leaving marks on the eggs. Is there any artificial coloring, etc, in what you are using for your geckos to lay eggs in? I'm not sure what it is, but just keep incubating it.
I had an egg this year, about 7 days in to incubation developed mold on about half the egg. I didn't have much hope for it. But for whatever reason, I decided to leave it in the incubator to see what happens.
That egg ended up hatching into one of the prettiest dreamsicles I have so far this season.
So my advice is to just leave it be, for the full incubation time.
I don't think there's much you CAN do at this point except sit and wait. What kind of perlite are you using? Is there anything added to it? Check the bag, maybe?
I use cocofiber as well and many of my eggs develop the same "stains". Just let them be and try not to handle them to much if at all, let them incubate unless they start to mold over or go way over the expected hatch date, I'm sure all is fine. I know how nerve racking breeding season can be, the most important lesson to learn is to just sit back and relax =)