Your issue with the tire is probably that the bead has not seated into the rim hook in that area. When that happens to me, I inflate the tire to desired pressure, and, by hand, force the bead into the hook by grasping the tire and rolling it upward from the rim in the affected area. Typically, it will gently ease into place.
If it is not a hook bead rim then I don't know the answer. Possibly the tube is pinched between the bead and the rim, in which case it is in imminent danger of blowing out and you should deflate & remount the tire immediately to prevent that.