Supercapacitor bank charging process breaks down dc/dc converter
The problem is the fixed 15v output voltage of your DC-DC converter. Capacitors should be charged with a current output, not a voltage output.

If the voltage on a capacitor is less than the output voltage of a power supply feeding it, it will take as much current as the supply cares to supply, in other words it behaves like a dead short. 

The DC-DC converter can still be buck, can still use the same power stage, but the controller should be changed to control the maximum current output to safe levels, as well as the maximum voltage to be safe for the supercaps.

With regenerative braking, ideally you would program the converter to put a braking torque on the wheels proportional to the position of the brake lever/pedal. This is naturally what you would get if you try to mimic the response of how mechanical brakes would behave, I presume you want the electric system to behave as a driver would expect it to behave.