This is the Bestiary, the complete list of enemies in The Legend of Zelda: Spirit Tracks.
Like in real life, Bees live in beehives, and are generally harmless. They will only ever attack Link if he attacks their home. Should you strike a beehive, accidentally or otherwise, the entire colony of bees will chase after you and attack, and all you can do is run away, either into a pool of water or into a building. They cannot be defeated. Sometimes, the remains of the hive contains Bee Larvae, a treasure worth 50 Rupees.
The Wrecker Phantom is one of the most useful, but also most dangerous, Phantoms. If one sees Link, it will roll into a ball, and roll at him with speed. They can destroy the yellow stone blocks found in the later floors of the Tower of Spirits, by rolling into them. Since they move mostly by rolling, they cannot carry Link when possessed by Zelda.