hands and feet are all small bones and are less rigidly connected together than the larger ones. They are often are lost when skeletons decompose, small animals carry the smaller parts off first, idk... I'd guess that it was simply an oversight / laziness on bungie's part. OR, perhaps they were hobbled and had their hands and feet cut off and locked in the vault to prevent the secrets from escaping. Maybe they were trying to get out and they got their hands cut off by the blast doors when they slammed shut. Maybe this was the set of SAW VLXI and they were handcuffed to the wall with an exotic hack saw and had to amputate their hands and feet to try and get out?