You are right about them usually only eating decaying tissue, but I am 100% positive the polyps were perfectly healthy on each occasion until they became a snack. I was shocked myself when I first saw it. I noticed some lashes missing and then I saw one of the amphidpods take a chunk out of one of the remaining lashes. I could see the neon green flesh he ripped off glowing in its mouth and go down his throat. I have witnessed this on a few seperate occasions spaced out over a 6-8 month period. I notice the problems would occur mainly after a week or more without feeding the tank and most damage done at night by always by a single large amphipod. Luckily, each time I was able to remove the offending amphipod with a turkey baster, and no more polyps would be affected after it was removed for several weeks or months. The first one was the hardest to catch and probably snacked on half a dozen polyps before I nabbed him. This leads me to believe that they don't do this on large scale and only a few tend to turn on healthy polyps.
Beerdrinker,
Mandarins are difficult to keep long term unless you can provide them with a quality source of live pods and are probably not your best bet.
There are several other alternative stalker type reef safe fish available that will control your pod population no problem. Most reef safe wrasses would work and would probably be faster than a slow poke mandarin.
I am not saying positively that this is your problem and it could be something else eating the lashes, and maybe you are just noticing the amphidpods because the polyps are retracting. I would still suggest trying a reef safe wrasse or other fish to reduce and naturally control the pod population. It wouldn't really hurt. The worst thing that would happen is having another mouth to feed. Good luck, I hope you find the source of your problems whether this is it or not.