Hi Behnam,
It sounds like you are getting different states (before SOC step) at different geometries. Especially when dissociating, many states become close in energy and it can be tricky to maintain a consistent set across different geometries. If you're using state-averaged MCSCF orbitals, maybe dynamical weighting would smooth some of the bumps.
Sudden changes may be physically correct, if they result from a curve crossing (adiabatic state changing character from one diabatic state to another). Of course, that would affect how you interpret the matrix elements.
Good luck,
Karl