The size of the section of Metropolis Brainiac takes, is much smaller than the one Superman saves at the end.
During Brainiac's attack on Metropolis, while in the Daily Planet, Lois takes a rolling chair, smashes it into one of the robotic sentries, sending it through a window.
It is shown the windows are clearly not floor to ceiling when the scene cuts back inside the Planet building. There's no way the robot could have simply rolled through the window.
The second time the bad guy fires the rocket launcher, he is holding it inside the helicopter. In the position he is holding it, the backblast would kill the pilots and destroy the flight deck.
While in Kandor, Superman smashes the ground several times in order to get Brainiac's attention. He lifts a huge chunk of ground to throw at one the robotic guards but, not only is there no hole where the chuck has come from, the ground beneath and around him shows absolutely no sign of damage.
Superman should not have any powers when he is inside Kandor. His attempt to fly should have been just that, an attempt. He shouldn't even have gotten off the ground. He also shouldn't have been able to break the pavement by pounding on it with his fists.