Wires made of topological insulators (TI) are a promising platform for searching for Majorana bound states. These states can be probed by analyzing the fractional ac Josephson effect in Josephson junctions with the TI wire as a weak link. An axial magnetic field can be used to tune the system from trivial to topologically nontrivial. Here we investigate the oscillations of the supercurrent in such wire Josephson junctions as a function of the axial magnetic field strength and different contact transparencies. Although the current flows on average parallel to the magnetic field we observe h/2e, h/4e- and even h/8e-periodic oscillations of the supercurrent in samples with lower contact transparencies. Corresponding tight-binding transport simulations using a Bogoliubov-de Gennes model Hamiltonian yield the supercurrent through the Josephson junctions, showing in particular the peculiar h/4e-periodic oscillations observed in experiments. A further semiclassical analysis based on Andreev-reflected trajectories connecting the two superconductors allows us to identify the physical origin of these oscillations. They can be related to flux-enclosing paths winding around the TI-nanowire, thereby highlighting the three-dimensional character of the junction geometry compared to common planar junctions.