I'm a little confused about the permissions setup. I can see that you can do magic.cast. to limit spell casting, but id like to limit certain players from using/crafting certain items/wands.

For example some players should not be allowed to use broomsticks.

Can this be accomplished?

Yes, this was missing from the Permissions page on the wiki but I added it recently. Sorry for the delayed response:

-Magic.use. : Player may not use a specific wand or magic item