that's interesting. Would it be okay if you could do more pullups than benching your weight? I can see how that might be bad the other way around.
First, I don't think you could ever do too many pullups or that doing nothing but pullups would cause a problem, since you are only using your body weight and pullups, like any exercise that moves the torso through space, require a lot of support from almost every other muscle in your body. That is why pullups are more taxing than pulldowns.
Second, if you are doing 12+ reps on either pullups or bodyweight bench presses (and you should if you are a reasonably fit male), it becomes largely an endurance exercise and not a strength movement, so the chance of muscle imbalance and/or joint/connective tissue damage is pretty low.