The materials issue sounds like the deconstruction teleport bug:
http://www.bay12games.com/dwarves/mantisbt/view.php?id=5994 It's a fairly well-known bug by now, but keeps completely baffling people who encounter it for the first time.
As for the "missing" dwarfs - DF currently has no concept for what we'd consider "missing", the tag just means "is dead but the dwarfs have not seen the act and have not found the corpse (yet)". They died somewhere out of sight and the corpses are hard to get at or no longer extant. Typical examples are when a dwarf ends up in a pit without an exit or falls into a river and drowns - in the first case, since the dwarf couldn't get out, a hauler can't get in to collect the cadaver, in the second, the corpse is somewhere in the river and not "safe" to get. There's no teleportation involved.
You can check for the location of mislaid corpses by going through the "stocks" z-subscreen, predictably under "corpses" at the end of the list. Expand the listing via <tab>, assuming your bookkeeper precision is high enough, check for corpses attritubted to your missing dwarfs (such corpses will be listed by personal name), "z"oom to the location to see where the corpse is. This often gives hints to what has happened and why the corpse hasn't been retrieved yet, e.g. if the corpse is underwater or in an inaccessible pit.
If there are no corpses with the correct names, the very bodies have been destroyed, which can afaik only happen through fire or if the dwarf or body was caught underneath a lowering drawbridge and smashed entirely.