I recently installed You Have To Name The Expansion Pack, but when I wanted to get down to some tinkering as an old character this happened. I currently have the n-Dimensional Lathe (which I don't actually own) selected, and in addition to the wands that should be displayed, it also displays several advanced reagents for Tinkering. They could still be crafted.
This is a known issue that occurs when craftDB.xml changes during a saved game. Starting a new character will fix it. In the meantime its an annoying bug, but you will still be able to craft those items if you have the requisite skill, even if you have to have the wrong machine.
Heh I was playing with craftDB a bit and noticed this. Didn't think I touched anything crucial. I noticed that even though the craftable is in the wrong machine, it still only requires the first machine. Example: I had the materials and recipe for a Clockwork Chainaxe, but it was in the Alchemy box (i didn't have an alchemy box at that point) I tried crafting anyway and it worked normally. However I did notice that the moved recipes can be added to the correct machine via bookshelves, which results in a duplicated recipe >.>. So the game forgets you know the recipe when it moves, but the recipe itself checks if you have the original crafting station. That's my guess anyway.