As for the Pentagon, there were plenty of eyewitnesses to the plane coming in. There was a book out right after 9/11, quoting journalists who covered the events of that day. One was sitting in traffic when the plane flew over the highway before hitting the Pentagon.
Basic physics. The fuselage, led with its nose cone, is like a bayonet, with the majority of the plane's weight piling up behind that narrow point of entry. Like a piledriver. The wings, relatively, have none of this. Additionally... additionally.... the camera captures show that the plane was on the ground a second or two before it made contact with the building, the wings with the fueltanks exploding (it appears to me) before full impact with the edifice.
At the time, NORAD relied on transponders to track individual planes. The terrorists turned them off. They could see the green blips on their screens but didn't know which were regular flights or hijacked flights. The airlines were not forthcoming at all. The military didn't even know for sure which plane hit the first tower till hours afterward. They also -- in hindsight -- took too long to ground all air travel. So, yeah if they know where a plane is headed or have a beacon on it. No problem. But trying to find a plane among the hundreds of others in a busy travel area? Wasn't happening.
There are also people who say what they saw hit the Pentagon did not look like a commercial airliner. I just find it a bit hard to believe that almost an hour after planes had hit the WTC, no local TV stations, amateur videographers or security cameras were in place to capture another jumbo jet hitting the Pentagon. You don't even have to question the size of the hole, outline on the building, or on-scene debris. That's a hell of a coincidence.