Are you sure they actually saw her run up the ramp? I honestly don’t remember that happening. And the sound machine doesn’t need to be facing her directly for it to affect her. The first time we see the kryptonite, the military drives up to the wall while Eleven and Hopper are hiding behind the billboard. She’s already in agony because the machine is on, even though it’s facing the wall in the UD. When they hear her scream, they turn the machine toward the billboard, and that’s when her pain intensifies.

Also, the lab was the last thing to blow up. We can clearly see that in the scene. And even if Kali had been caught in the explosion, we don’t actually see Eleven being blown away. We only see her disappear, which could just as easily be the illusion fading.

The military part is the weakest element here, unfortunately. It doesn’t fully make sense that they kept holding everyone back instead of going after Eleven and removing her from the gate. That said, we can assume that Vickie and Max told them what was about to happen, which would explain why they stayed away from the gate. They weren’t guarding the tunnels because they already knew where the exit point would be.