How can Naruto characters teleport/disappear?
From what I understand, there are only actually a few ways to teleport. Those include Tobirama/Minato's Flying Thunder God technique, reverse summoning, and Obito's space/time Sharingan based technique.

Most of the time, when shinobi just poof, that means it was either a clone or they travel at a high speed such that one can not detect their movements. If it was a clone, then it was always a clone to begin and the person did not just substitute himself for a clone.