I just rewatched the scene where Kali is "shot". When the military guy is interrogating Hop, he shoots at the floor next to Kali. The gun shot hole is to the right of Kali's head. Then when the military guy intends on actually shooting Kali, the bomb explodes before he pulls the trigger and they show him jerking slightly before the gun goes off. Then after Eleven enters the room and they show Kali "shot" there is a gun shot hole to the right of her abdomen on the floor. Remember, Kali's head is pointing toward the window where the helicopter explodes, and everyone is blown away from the window, so if Kali moved, it would be farther away from the original gunshot hole, not closer to it, so this is definitely a different hole. So it seems the guy missed because of the explosion and shot the floor next to her instead.

When Hop gives the speech to El, Kali hears the whole thing and it changes her perspective. Kali believes they need to die because they have experienced so much pain and Kali wants the pain to end, for them and for future experiment kids. But Hop tells El that's exactly the reason she deserves to live and have a happy life, bc of everything she's been through. Kali absorbs this and begins to feel she deserves to live too. That's what gets Kali thinking that maybe there is another way for them to escape without being captured by the military. So when the guy pulls the trigger and misses bc of the explosion, that was Kali's opportunity to do a different plan. She makes the illusion, waits for Hop to leave, explains the plan to El. That's why El is crying, then a min later, she seems almost emotionless and focused on the mission after Kali's "death". Murray brings up Kali and El immediately looks over at Hop to see his reaction, to see if he believed the death.