Revealing mistake: When Zod is arrested, his bloody facial wound is a glued-on prosthetic.
Revealing mistake: At the end when the drone crashes in front of the car and the soldier gets out you can see the footprints in the sand from previous takes, in the exact spot where he steps.
Answer: When Jor-El stole the Codex, Zod and his followers were not yet sent to the Phantom Zone and Krypton had not begun its destruction. Jor-El was opposed to Zod's plan to use the Codex. Once Zod's rebellion against the council had begun, Jor-El stole the main Codex and hid it with Kal-El. While Jor-El knew Krypton would be destroyed, he didn't know when and wanted to prevent Zod from using the Codex as planned. Zod then killed Jor-El, the council regained control and ended the rebellion, and then sent Zod and his followers to the Phantom Zone (not knowing or believing Krypton was going to be destroyed).
Bishop73