We compare the molecular and ionized gas kinematics of two strongly lensed galaxies at z~1 that lie on the main sequence at this redshift, based on observations from ALMA and MUSE, respectively. We derive the CO and [OII] rotation curves and dispersion profiles of these two galaxies. We find a difference between the observed molecular and ionized gas rotation curves for one of the two galaxies, the Cosmic Snake, for which we obtain a spatial resolution of few hundred parsecs along the major axis. The rotation curve of the molecular gas is steeper than the rotation curve of the ionized gas. In the second galaxy, A521, the molecular and ionized gas rotation curves are consistent, but the spatial resolution is only of few kpc on the major axis. Using simulations, we investigate the effect of the thickness of the gas disk and effective radius on the observed rotation curves and find that a more extended and thicker disk smooths the curve. We also find that the presence of a strongly inclined (>70{deg}) thick disk (>1kpc) can smooth the rotation curve because it degrades the spatial resolution along the line of sight. By building a model using a stellar disk and two gas disks, we reproduce the rotation curves of the Cosmic Snake with a molecular gas disk that is more massive and more radially and vertically concentrated than the ionized gas disk. Finally, we also obtain an intrinsic velocity dispersion in the Cosmic Snake of 18.5+/-7km/s and 19.5+/-6km/s for the molecular and ionized gas, respectively, which is consistent with a molecular disk with a smaller and thinner disk. For A521, the intrinsic velocity dispersion values are 11+/-8km/s and 54+/-11km/s, with a higher value for the ionized gas. This could indicate that the ionized gas disk is thicker and more turbulent in this galaxy. These results highlight the diversity of the kinematics of galaxies at z~1 and the different spatial distribution of the molecular and ionized gas disks. It suggests the presence of thick ionized gas disks at this epoch and that the formation of the molecular gas is limited to the midplane and center of the galaxy in some objects.