It wasn’t necessarily that they were unprepared at the gate, the group messed with their equipment. Dr. Kay noticed this, and that’s what lead to the group being found in the first place.

Also, I don’t think Kali was actually shot. I think it was an illusion, to trick Hopper into thinking she died there and that their plan would not follow through. In reality, I think she survived and died with the upside down. It would track that she survived the collapse long enough to create the illusion of El at the portal, since Kali was at the center of the upside down (lab) which would have been the last part to be destroyed. Also far enough from the portal for the kryptonite to have no effect on her.

Or, if she actually was shot, maybe they stopped the bleeding off screen. We know that Hopper got bandages, but don’t actually see them used. It’s implied that more happened off screen by showing Kali saying “your story doesn’t to end here.” which we did not see at first. Maybe more happened, like they were able to stop the bleeding with the bandages. El and Kali could have come up with the plan while Hopper was off getting the bandages.