  We investigate the Josephson effect in a bilayer graphene flake contacted by
two monolayer sheet deposited by superconducting electrodes. It is found that
when the electrodes are attached to the different layers of the bilayer, the
Josephson current is in a $\pi$ state when the bilayer region is undoped and in
the absence of vertical bias. Applying doping or bias to the junction reveals
$\pi-0$ transitions which can be controlled by varying the temperature and the
junction length. The supercurrent reversal here is very different from the
ferromagnetic Josephson junctions where the spin degree of freedom plays the
key role. We argue that the scattering processes accompanied by layer and
sublattice index change give rise to the scattering phases which their effect
varies with doping and the bias. Such scattering phases are responsible for the
$\pi-0$ transitions. On the other hand if both of the electrodes are coupled to
the same layer of the flake or the flake has AA stacking instead of common AB,
the junction will be always in $0$ state since layer or sublattice index is not
changed.
