Michael has always hated Toby because he has no power over him and can't control Toby like he can the others. Toby is more level headed and will refuse to do some of the silly things Michael insists on doing.It's basically a power play that you see in every organisation in the world.

Toby always shoots down Michael's silly random ideas. Also, Toby works in HR, so Michael isn't really his boss and he can't do anything about it.

remember this is just a TV show. It is purely speculative in the minds of the writers to make the show more interesting. It is a spoof on reality TV shows and is not meant to depict real life ....only to exagerate real life situations for comedy.