If you run a Spacegroup analysis on this crystal structure, it comes out as Monoclinic. It just so happens that your initial structure has the angle 90 degrees but that can be seen as a special case of a monoclinic lattice. So since the space group is constrained (number 15), it is free to relax this angle. If you want the lattice to remain hexagonal, you need to make sure the symmetries of the atoms actually correspond to a hexagonal space group.
I am not sure what Nb2S4 crystal this is supposed to be... The Nb-S bond length is very large (3 Å) compared to the more common compounds with Nb and S, where the bond is about 2.5 Å only. Are you sure the structure is correct? You can search for and download several Nb+S structure from the Materials Project database within NanoLab, maybe check these out.
