Are you in high school or college? In season or preseason? I am guessing that he has done or heard of that Px90 or whatever those informercials are on television? Muscle confusion is a term that is widely misused and totally misunderstood by most people, and if your coach is like a math teacher or something, he is woefully uneducated.
What exactly is it that he wants you to do? You said you previewed it already. Can you describe the routine? There is really nothing wrong with mixing up a core workout, keeps things fresh and not so boring. Hopefully this is all that he is doing. Most teams do the same stupid core exercises and then do them improperly. I do not know what type of a relationship you have with your coach, or his training, but you really need to ask lots of questions while you are learning this. Things like "what muscles are we working.....is THIS where I am supposed to be feeling this exercise?" And "Is this the proper form?" If he can't answer those questions then he has no business making you do a new routine. You have a relationship of trust with your coach, and if he is not qualified to do this properly, you can become injured.
But...on the other hand,it could be a great new routine for your team. THere is absolutely nothing wrong with having a strong core, and will only benefit your running. And I seriously doubt that any of you will bulk up. Muscle mass is just an expression for building muscle....it doesn't mean bulking up. Unless you are a muscular guy to begin with and lifting some serious weight, you will not be getting large.
But be careful and speak up right away if you have questions.