What you are seeing in both cases is the Havok physics of the engine.
All objects interact with the engine using collision, which tells it how to act in game. For example, all architecture have "static" collision - immovable, impenetrable, clutter has less rigid type of collision that it can be manipulated in the game.
In the case of the potion bottle, it was never meant to interact with in the game, it was only a mesh to be visible in your inventory. This is why it's spinning oddly when you put it in the game. If you want to use that mesh, it needs to have it's collision remade so that it's similar to other clutter items. You can do this one of two ways: 1. In NifSkope, copy the two NiTriShape branches of the bottle, and paste it into another regular potion bottle mesh (that you know works in the world), then delete the original bottle of that mesh, or 2. In NifSkope, delete the branch bhkcollisionobject (the collision), and remake it by highlighting the NiTriShape of the bottle, right click > havok > create convex shape. This will give you the framework, you'll have to open another potion bottle mesh and go through each option to make your new collision the same as the existing example.
In the case of the alchemyworkstation mesh, that's a complex mesh and not a good idea to try to take one piece of it and turn it into something else in NifSkope. This would be a job for a 3D editing app.