No initiative never takes over move order, and the second part of your question, there is slow and fast buffs, for example most npcs have permanent slow buff in plot missions and some have fast buff like Deidara and Chikushodo in Hidan SA, in pvp only ninja we have that can do this is Kurotsuchi.

So if your example happened in normal pvp, it was most likely a result of lag, if it happend in pve they probably had slow buff.