Not a pilot but familiar with the aviation world and procedures.
Obviously the plane had issues getting off the ground. Probably because it was too heavy. Typically, pilots calculate a speed beyond which they can no longer safely abort the takeoff. Beyond that speed, the plane is basically going to fly or shoot off the runway and crash. That point is decided based on weight, wind, runway length, etc. It's entirely possible mistakes were made with that or with loading the plane. Maybe there was some wind shear as well, which could explain a sudden drop or unexpected challenges getting off the ground.
Usually the co-pilot's job is to call these speeds out and if either of them calls to abort, there is supposed to be no discussion or debate on this and pilots are trained to act right away because every second counts. Obviously that did not happen
So, the pilots were not aware of issues before the abort speed (or they should have aborted) and committed to getting off the ground. I'm sure the in cockpit recordings will be part of the investigation. They sort of succeeded in the sense that they hit some objects but ultimately did not crash and got off the ground. Their climb rate must have been terrible. Usually the gear comes up as soon as you have a positive rate of climb (reduces drag). I imagine they called gear up seconds after leaving the ground before they hit anything even and the gear was likely transitioning.
Wind shear could have caused enough change in airspeed to cause the plane to not climb or even descend a bit. A heavy plane would have used up most of the runway in any case.
They then proceeded with what looks like normal procedure to get to altitude. Presumably they would have almost climbed out and changed frequencies from tower to local traffic controllers after 20-30 seconds or so. Recordings of that are going to be interesting. Presumably the damage to the ILS equipment would not have been noticed right away on the ground and people would have needed some time to figure out what the hell happened and what caused it and what plane hit it. Likewise the damage to the wall would not have been reported right away. By then the plane would have transitioned out of their area.
The question is whether the pilots noticed that they hit any objects and what the communication was with these controllers on this. The plane would have been pitched up (restricts visibility to the ground in front of you) and the damage occurred pretty far behind the pilots. So they may not have seen the obstacles immediately in front of them or heard/felt hitting them. These planes are big and heavy and there's lots of noise and vibrations when a plane takes off.
The damage looks dramatic but you wouldn't be able to see it until after the landing. Obviously the plane was flying and climbing and cruising normally. And they also landed safely. So flight operations seem to not have been directly affected. So, I can see them concluding that they had a stressful takeoff but had gotten in the air successfully. Then some time later they got the news that they hit some obstacles and that there is probably damage to the plane.
The big question is why that took 3 hours. I imagine it involved a lot of communication on the ground.