Yep... fungus and such can be a problem, but those are fairly visual with either closed polyps with white zit like growths or a brownish film on the polyps.
These appear to irritated or damaged.
Acat.. the ones that looked like they are flipped over (skirts) are they bending back over on themselves are actually missing skirts?
The ones that are closing up... are they pinched closed with the colored portions sticking out or are they chewed off?
What kind of light and flow are they in?
If you can remove the colony and inspect it, see if you can see any missing polyps or missing flesh etc.
You could have some worms or pods chewing on these.... I doubt any of the fish you listed would be likely to do that.
You might also pull them out, give them a good 5 minute dip in fresh water that is the same temp as the tank and see what falls out. It doesn't look like nudie or sundail damage, but there are other things such as fromians etc that could be doing it or asterina stars etc.
