Hi Mehrosadate,
This is the result of a numerical integration error. QuTiP doesn't automatically check for convergence and doesn't always select a sufficiently small integration step size. It uses a few heuristics but they don't necessarily work for some complicated Hamiltonians.
Importantly, the number of steps in taulist doesn't usually affect the integration step size. Instead, you should pass the Options() class to the coherence_function_g2() function. Decrease the max_step and increase nsteps and you will eventually get a smooth positive function for this simulation.
The other option (which I highly recommend here) is to change the solver from 'me' to 'es'. The eseries solver decomposes the time evolution of the master equation into exponentials, which works very well for steady state problems like this (and basically removes all numerical artifacts).
Kevin