That looks like red slime algae, cyano bacteria. It is a real pain to get rid of. High nutients in the water, poor lighting, lack of current are all causes. I would suggest making sure your skimmer is working good, do a water change or two and increase current to the affected areas. Make sure you are not over feeding. High phosphates and nitrates is a big cause also. There are also chemicals you can buy to get rid of it, but that doesn't fix the cause of it. If you go that route, your skimmer goes crazy, at least mine did. I tried Red Sime Remover and it did a good job. My flowerpot coral didn't like it much but has recovered just fine. The rest of the inverts showed no stress. There was a good thread on this topic about a week ago in the disease forum started by golfish. Do a search and you can get more ideas by people who have more experience with it then I do.
Oops, I just checked and the topic started by golfish is still current. Just scroll down on the disease forum.
