So I have had Pagoda cups for years and here is what can cause them problems. In the wild they are found in clear water areas where there are no sand that can blow up on them.
So in your case I can see a path in the areas having a problem. This can cause an infection. I treat this with a lugols dip treatment to kill off the bad bacteria that is eating the flesh of the coral.
Do you have the coral on the sand bed or do you have a sand bed? If so move the coral up off the sand bed and give it good flow. The coral loves good flow across it. Has you coral always been contracted.
Mine is a super bright Green and bushy. Do you feed the coral I always feed coral food at least several times a month.
With a sand bend bottom is there fish picking up or blowing sand a round the coral. The coral doesn't remove sand will and the sand will cause infection as there is no way for the coral to deflate and move the sand off its skin. Which will cause infections. I had a fish that started blowing sand up on the coral and I had to move the coral to keep the fish from constantly putting sand on the coral.
I bet a fish is causing the issue but you will need to watch the tank to see the one doing it.
