For a system, the bodies within the system exert forces of action and reaction on each other. So F12 +F21 = 0. For a pair of bodies in the system.
It should be remembered that the work done by the action reaction pair need not always cancel. The distance travelled by the two bodies of different masses in coming to rest, when allowed to move until their mutual force is not necessarily same. So W12 W21 ≠ 0.
However in some cases, the work done by the action–reaction pair is zero.