Two things must be understood here. The first is that the World of Nekudim came into existence when the World of Atzilut first began to take shape, before it was complete. Atzilut was then like a vessel whose form was as yet incomplete. The second thing that must be understood is that the World of Nekudim is not to be identified with the World of Atzilut itself. Rather, it is what emerged while the form of Atzilut was still incomplete.
Thus the Zohar states: “When the Craftsman pounded with the iron hammer, it produced sparks on all sides, and the emerging sparks came out as flashes that lit up and were then immediately extinguished, and these are called the Primordial Worlds, and because of this they were destroyed and did not endure...” (Idra Zuta 292b).