At our shul which is Orthodox (Lubavitch) they take the the Sefer Torah down the women’s side of the Mechitzah on its way back to the Aron hakodesh some freinds of mine say this is problematic. I have never seen any other Chabad or Orthodox shuls do this. Are there any issues with this and if so what are they.

I have seen this custom in many orthodox shuls. Where it is the custom it is fine. There are communities which have the custom that a woman who is a niddah does not touch the sefer Torah, but this is a strict position and a community that follows the lenient position certasinly is within the halacha.