It's probably the gobies. Gobiodons will clear patches of Acropora for nesting sites, but I've found that sometimes in captivity, they develop a nasty habit of eating acro polyps the whole time. Happened to me and I'll never try Gobiodons again.
I've caught mine in two ways. One was to use a large nylon mesh bag and surround the Acro head the goby was hiding in, using a chopstick to force it into a portion of the net where I could seal up.
The other way sounds a little cruel and I'm not sure I'd recommend it, but it worked. I siphoned the little goby out! 8O