We study the origin of misalignments between the stellar and star-forming gas components of simulated galaxies in the eagle simulations. We focus on galaxies with stellar masses ≥109 M⊙ at 0 ≤ z ≤ 1. We compare the frequency of misalignments with observational results from the SAMI survey and find that overall, eagle can reproduce the incidence of misalignments in the field and clusters, as well as the dependence on stellar mass and optical colour within the uncertainties. We study the dependence on kinematic misalignments with internal galaxy properties and different processes related to galaxy mergers and sudden changes in stellar and star-forming gas mass. We find that galaxy mergers happen in similar frequency in mis- and aligned galaxies, with the main difference being misaligned galaxies showing a higher tidal field strength and fraction of ex-situ stars. We find that despite the environment being relevant in setting the conditions to misalign the star-forming gas, the properties internal to galaxies play a crucial role in determining whether the gas quickly aligns with the stellar component or not. Hence, galaxies that are more triaxial and more dispersion dominated display more misalignments because they are inefficient at realigning the star-forming gas towards the stellar angular momentum vector.