Ball joints and control arm bushings were a weak spot in the E36 design, but I thought that was remedied with the subsequent 3 series platforms, perhaps not. In any event, 50,000 miles seemed to be the general rule of thumb for ball joint life, maybe longer for the bushings, of course depending upon how the car was driven, so I don't know where that puts you with the present mileage you have on the car. I haven't heard of the term "torn" control arm bushings before though, worn yes, but "torn" no, so I don't know what they mean by that.
I hope you have some written documentation as to what your warranty coverage is, because this "certified" term is rather meaningless, more a sales pitch than an enforceable coverage for a used car (there have been legal cases about this); complicating the matter further is that you bought this car from a non-franchised place, and while the onus seems to rest with them (they seem to have sold you that car based on its "certified" condition) I don't know how the legalities shake out. Unfortunately I think you have some yelling and screaming and threatening to go through to get some sort of accommodation.
On the somewhat up side of things, you can get yourself some greater peace of mind and much longer mileage with the bushings by upgrading to stronger M3 types, or even going to M3 control arms with the bushing. The reason for the latter move is that replacing the bushings just themselves can be a royal and costly pain, whereas for about the same or even less money considering the labor involved you can just replace the whole control arm and be on your way. At least this is what's possible for the E36 chassis, I assume but am not sure that that can also be done with the later chassis.