Boyfriend, obiter.
First thing, this is a UK site and I don't know how tenancy laws work in the US where I guess you are - but here, if the three of you sign a tenancy agreement, the landlord doesn't expect anyone else to live there - which the boyfriend now is, in effect.
You have to get together, the three of you, arrange a formal meeting if you have to - because there's more to this than just the SO. You all three need to be dibbing in with rent, household costs etc - no wonder your friend thought it was all so great, if you were bankrolling her to start off with - and now there's another body in the house, either he needs to get work to pay his way, or she has to pay another quarter (i.e. for him too). You have to be firm and let her see that she is taking advantage of your friendship, and that the original deal was for her to share with you, not four people. If she doesn't like it, she can move out. First off though, check your occupancy agreement and see what it says about movng in a fourth person - if the landlord doesn't know he's there, that's a good place to start.