The reasons for not automatically selecting a reserve braking source may vary, but yes, if you have a loss in one system, connecting another system to the place that's experiencing the loss may not be the best choice.
It's more complex than that, however. In our aircraft (B747) for example, a number of functions are tied to the tilt of the landing gear. The landing gear is tilted to get it into the gear wells during retraction, but tilting the landing gear employs switch logic which also tells many aircraft systems what to do; it puts the airplane into "flight mode." Among the features of the tilt logic are touch down protection; a feature that dumps brake pressure upon touchdown to prevent a skid when the gear first touches. Reserve brakes disable this tilt logic function.
In our case, normal braking comes from system 4, or system 1 (depending on which is selected by the flight engineer. A massive fluid loss in either case should activate a hydraulic fuse which limits fluid loss, but automatically applying yet another system isn't something we necessarily want to do. Additionally, where the normal braking applies antiskid to all the wheels, our reserve brakes only apply it to axle-pairs of wheels, reducing braking effectiveness and applying other considerations, too.
In any event, before we ever arrive at the need or reserve brakes, we have the option of using either one of two systems to operate the brakes normally. Either of those systems must be manually attached to the brake system by a switch on the flight engineer panel. Just as the normal systems must be manually selected and connected to the brakes, the reserve brakes must be also. Admittedly, our Juraissic Jet isn't state of the art any more, but it gives you a general idea to answer your question. Different airplanes and different systems operate...differently. The main point is that there's some complexity to the system, and the choice of employing it, therefore, is best left as a pilot decision.