Trying to craft a Cookery and I have the stems yet it says I do not. Same was happening for the Glands, I had to put them in my inventory but did not have to put other stuff in my inventory. I have stems on a palette beside me. I cant hold 9 stems so that's pointless. Therefore cant craft a cookery. 

To craft the cookery, you need to place it down with the Construct option and then add the stems. Just like everything else you build in this game. You don't need to have all of it in your inventory the moment you want to place it down in the world.

I personally think this needs updating. I mean if the game can detect other items in storage boxes/chests then it should detect stems and walls on pallets or any the player is holding, this will save so much time going forwards and backwards. I’m surprised  it doesn’t work this way already.