While the exact factorization has offered a new framework to develop new trajectorybased methods, capturing quantum (de)coherence effects in a variety of photochemically interesting systems from first principles, these methods are not immune to the breakdown of physical constraints such as energy conservation due to approximations made in their derivation. The coupled-trajectory mixed quantum-classical (CTMQC) algorithm was the method that was derived first and, at its core, consists of an ensemble of classical-like trajectories that are coupled throughout their dynamics. Such coupling provides new mechanisms to correctly reproduce quantum (de)coherence effects. A modification in the algorithm was recently proposed, dubbed CTMQC-E, which restores energy conservation for the ensemble of coupled trajectories . In this work, we extensively analyze the extent and implications of energy (non)conservation in CTMQC and in CTMQC-E with a detailed study of electronic and nuclear properties for a variety of molecular models parametrized to reproduce the dynamics of a set of molecules with different features, e.g. different topologies of conical intersections and of growing complexity. We study the ultrafast dynamics through a 2-dimensional conical intersection in bis(methylene)adamantyl (BMA) radical cation, butatriene cation and pyrazine, the photoisomerization dynamics of 2-cis-penta-2,4-dieniminium cation (PSB3) and the photo-relaxation dynamics after photo-ionization through a 3-states conical intersection in the uracil radical cation.