Spots can usually be one or two things. Either it is getting bit by another rat which can be dressed with a little dab 'o' neosporin or bacitracin or teramycin ointment once they are seperated or they have mites. Mites are like fleas. They suck blood. You can see them around the ears and eyes if you have an infestation. It is a cage and animal problem. You will have to clean the cage totally and replace all the bedding and also wash the animal warm water. A little anti-mite spray in the water may help. Rats generally do not like this but it is necesary, like a flea dip. You may also put some ointment on the ears if there is a lot of irratation.
They also make anti-mite strips you can put in the cage which kill mites. THese are not my favorite because they are usually potent and should not be left in the cage for more than a 1/2 hour to an hour at a time