For some reason the when the script below runs, my dropper model and my door part switch places. I can't figure out why for the life of me. The door shouldn't even be able to get or use the dropper position. The objects I'm cloning are in the same exact hierarchy as the original plot, so I don't see that being a reason. Any insight as to how this works would be greatly appreciated.

game.Players.PlayerRemoving:connect(function(player)
	if(player == Owner) then
		local doorClone = game.workspace.cloneParts.GetOwner:Clone()
		doorClone.Parent = script.Parent.Parent.Parent

		for index, child in ipairs(script.Parent.Parent:GetChildren()) do
			childOrig[index] = child
			
			if (childOrig[index]:IsA("Part")) then
				childOrigPos[index] = childOrig[index].Position
			
			elseif (childOrig[index]:IsA("Model")) then
				childOrigPos[index] = childOrig[index]:GetModelCFrame().p
			end
			childOrig[index]:Destroy()
		end

		for index, cloned in ipairs(doorClone:GetChildren()) do
			childClone[index] = cloned
			
			if (childClone[index]:IsA("Part")) then
				childClone[index].Position = childOrigPos[index]
			
			elseif (childClone[index]:IsA("Model")) then
				childClone[index]:MoveTo(childOrigPos[index])
			end
		end
		GetOwner:Destroy()
		print('cloned')
	end
end)

:GetChildren() returns objects in no particular order. You should never use the index that you get from iterating over it.

Instead, use the child as the index for the original position

Code cleanup

It's not idiomatic to use () in conditions in an if.

You shouldn't use childOrig[index] to refer to child

You shouldn't use childClone[index] to refer to cloned

You're trying to compare objects between two different models. That's difficult to manage correctly (what if the models were completely different models?) Your code can't easily enforce that they're the same.

Really, you should copy from the representation that you created; by iterating over childOrig and creating new children and putting into a model (rather than cloning a model and trying to find the corresponding things in the map)