While the original coupled-trajectory algorithm derived from the exact-factorization, i.e., CTMQC, was derived from first-principles, the approximations introduced result in some exact conditions not being guaranteed. In a similar spirit to the fix made in CTMQC to ensure the physical condition of zero trajectory-averaged electronic population transfer when the NAC between pairs of states is zero, CTMQC-E was proposed as a fix on CTMQC to ensure energy conservation over the trajectory ensemble, extending an idea proposed for independent trajectories in Ref. [ 41]. Correcting the trajectory-averaged energy may have a significant effect on general observables of the system, nuclear and electronic, and our results here have explored this over a range of systems where the electronic and nuclear dynamics are strongly and non-trivially coupled after a photo-excitation. In this work, we used the G-CTMQC 52 code to compare CTMQC-E with CTMQC and with surface hopping (with energy decoherence corrections) as well as to validate the accuracy of the correction towards energy conservation. We employed several molecular models that offer a broad test-bed for CTMQC-E, involving two-state or three-state conical intersections, two, three and eight (with 36 Cartesian coordinates) vibrational modes, and with and without periodic boundary conditions. In all cases, CTMQC-E efficiently improves energy conservation with respect to CTMQC, thus allowing us to expect stabilization of the dynamics at long times, particularly for the nuclear observables. In some cases, however, electronic observables are affected in such a way that they deviate from the CTMQC and from the reference, suggesting that there is still room for improvements and novel developments. Future work includes, for example, using other directions for the redefined accumulated force in CTMQC-E to ensure energy conservation, and the possibility of tuning the CTMQC-E correction only in certain ranges of energy deviations, while using the original CTMQC when the total energy is well-behaved.