What is the total energy stored in the capacitors? Shouldn't the repulsive potential energy stored be included? Is there the repulsive energy stored in the capacitors or that energy is already included in the conventional calculation of the stored capacitor energy?
 A: Assuming no dissipation, the energy stored in a charged capacitor equals the work done in charging the capacitor.
But the work required to increase the charge $Q$ of a capacitor by $\Delta Q$ increases with $Q$; the more charged a capacitor is, the more work is required to increase the charge by $\Delta Q$.
You might think of this in terms of repulsion, i.e., the more excess electrons there are on a plate, the more work is required to add one more electron to the plate.
So, in this sense, repulsion is included.
A: Let's consider a spherical capacitor. The inner sphere has the radius a and the outer sphere has the radius b. Suppose the capacitor is already charged and we are trying to calculate all the electrostatic energies inside the capacitor. If the inner sphere is charged by -Q and the outer sphere is charged by Q, there will be attractive force between the inner and the outer sphere. But then there will be repulsive electrostatic potentials on each spheres because same charges repel each other. I think this repulsive electrostatic potential has been neglected and not included in the conventional text book presentation. 
A: One more thing to add is that the attractive force is in the radial direction from the mutual center of the spheres, while the internal repulsive force inside the spherical shell is tangential to the surface which means that the two forces ( radial and tangential) are orthogonal to each other. Therefore they can not be mixed. 
