Using an extended Lewenstein model under single-active electron (SAE) and linear combination of atomic orbital approximations, we perform a theoretical investigation of the high harmonic generation (HHG) spectrum of diatomic molecular systems in intense short-pulse laser fields. The wavelet transform and Wigner distribution, two complementary time-frequency methods, are extended for the exploration of the underlying mechanisms responsible for the fine structure of HHG peaks in the plateau regime. We found that, under some conditions, the HHG fine structure is mainly due to the interference between the long and short trajectories. The extension of the cut-off in the molecular HHG spectrum is also observed when the internuclear separation is large. Detailed analysis shows that the one-centre and two-centre terms contribute, respectively, to the low- and high-energy parts of the molecular HHG spectrum.