Yeah, they are fine. Some spots will wash off (not that I've ever bothered, I think they are kind of pretty) and some won't. Some are drops of blood that have gathered on the shell during the eggshell forming process. Some are excess eggshell color pigment.
They are harmless and make the egg basket that much prettier
I wouldn't worry unless you start seeing copious amounts of blood on the eggs or on the hens bottom.
I was getting the same thing, I think it was from putting them in the sink and going back later to wash them. Either from them sitting in one spot for awhile, or sitting in water. Does it look like this?