I see this a lot, too. It's pretty noticeable in dwarf therapist, since it highlights this sort of thing in the "Equipment" column. It seems to happen when I'm making new armor, so the dwarves at the top of the list grab the new, high quality shiny, and hand down their medium quality to the next one on the list, who hands down his stuff. So every soldier in your fort ends up with new armor assigned. But they don't actually change their armor until they go on duty.
So a dwarf in the middle of the list gets assigned a better helm and goes on duty. He takes off his old helm, but his new helm isn't available because it's former owner is off duty and is still wearing it, so now he has a bare head. Or maybe the new helm is still in the forge, unavailable because it is waiting to be picked up by the weakest dwarf in the fort, carrying a very full armor bin.
One.
Tile.
Every.
Two.
Seconds.
In fact, that bin probably holds half the armor in the fort, and most (if not all) of my soldiers are assigned stuff in that bin. So they're all standing around half naked waiting for a chance to get their armor.
Oh, and by the way, a vile force of darkness has arrived. Now it's a race to see if the armor bin gets down to the forge and back up to the stockpile before the goblins get into the fort to fight my half naked soldiers.
I think it's time to rearrange my standard fort design so the armor stockpile is next to the forges, not next to the barracks. Or maybe just make it a lot bigger and set bins to zero.
But that still won't solve the problem of off duty soldiers breaking the chain of hand-me-downs. The only way I know to deal with that is to periodically station the squad in the armor stockpile (while an armor bin isn't in transit) and set them each to have armor replace clothes, then set them back to wearing armor over clothes. Pain in the backside. Especially when you haven't done it in a while and an ambush uncloaks and you suddenly realize that half your soldiers don't have half their armor.
If you just have armor replace clothes and you're short on some armor bits (because you just expanded your military and are in the process of making more), then those who don't have greaves yet take off their trousers anyway. And if you just set it to wear over clothes, they won't put on their helmet because it doesn't fit over their pig tail fiber cap and sheep wool hood. But if you have them replace, then wear over, they'll wear all the armor they have, plus whatever other clothes will fit.
Keith