Dear Rajesh,
There is a limitation in the code right now for symmetries in non-collinear calculation that removes the improper symmetries when you have some, we are working on this limitation right now…
So the calculation is not wrong as it uses less symmetries than it should be, but it will be longer because of that. It can be problematic if you have an unstable phonon mode or an electronic instability in the symmetry you want to work with that the lower symmetry allows to relax, as your system will go to this lower symmetry phase if you relax, but if your system is locally stable under those symmetries it is OK (and it is the case in your system if Iḿ right).
Best wishes,
Eric