We investigate the role of the pairing field dynamics in low-energy heavy ion reactions within the nuclear time-dependent density functional theory extended to superfluid systems. Recently, we have reported on unexpectedly large effects associated with the relative phase of the pairing field of colliding nuclei on the reaction outcomes, such as the total kinetic energy and the fusion cross section [P. Magierski, K. Sekizawa, and G. Wlazłowski, arXiv:1611.10261 [nucl-th]]. We have elucidated that the effects are due to creation of a "domain wall" or a "solitonic structure" of the pairing field in the neck region, which hinders energy dissipation as well as the neck formation, leading to significant changes of the reaction dynamics. The situation nicely mimics the one extensively studied experimentally with ultracold atomic gases, where two clouds of superfluid atoms possessing different phases of the pairing field are forced to merge, creating various topological excitations, quantum vortices and solitons, as well as Josephson currents. In this paper, we present unpublished results for a lighter system, namely, $^{44}$Ca+$^{44}$Ca. It is shown that the pairing effects on the fusion hindrance are rather small in lighter systems, due to a strong tendency towards fusion, which is consistent with an earlier study.