Phase-locked WDM superchannel transmission systems have been demonstrated to effectively provide reduced DSP complexity. Nonetheless, the subchannels may be affected by laser and nonlinear phase noises, which can be effectively compensated using joint carrier phase recovery (JCPR) techniques. In this work, for the first time, we demonstrated via extensive numerical simulations that the subchannels experience intra-channel dispersion-induced phase-offset (DIPO), which significantly degrade the phase coherence and hence performance of JCPR schemes. In addition, we described in detail and identified the origin of DIPO as the interaction between the LO laser linewidth and the dispersive walk-off effect among the subchannels after long-haul dispersion-unmanaged fiber transmissions. Comprehensive simulation results revealed that the channel spacing, fiber length and the number of subchannels within the superchannel enhances the DIPO. Consequently, the effect of DIPO on JCPR performance is severe for all outer subchannels than the inner subchannels. Finally, we proposed and demonstrated a modified JCPR where simulation results showed that the BER limit for soft-decision FEC could still be achieved in a 50 GHz-spaced 5-channel 45 Gbaud 16-QAM phase-locked WDM superchannel transmission system over a 3000 km fiber link with phase noise effects from both laser linewidth and fiber nonlinearities.