A brief summary of the programme:

The USAF could not prevent the attacks because transponders in the hijacked jets were turned off. Explosives in the twin towers were "debunked" by Popular Mechanics (now there's a joke). The demolition of WTC 7 was also "debunked" by the ever reliable Popular Mechanics. The rest of the programme was dedicated to straw men. Was the Pentagon was hit by a plane? Did Flight 93 crash in Pennysylvania or did it land elsewhere? Did 4000 Jews skip work in the WTC on 9/11? Were the attacks predicted in the pilot of the "Lone Gunmen" TV show? Finally, the programme finished with an irrelevant piece on pre-9/11 warnings which were missed.

The conclusion of the BBC: the evidence doesn't support conspiracy theories.

Okay, let's take a look at a some facts which were "overlooked" by the BBC.

Fact: FEMA was in New York on September 10.
http://whatreallyhappened.com/fematape.html

Fact: Odigo workers received warning of the 9/11 attacks.
http://www.whatreallyhappened.com/odigo_9-11_warning.html

Fact: There were bombs in the WTC buildings.
http://whatreallyhappened.com/911_firefighters.html

Fact: The Office of Emergency Management issued a collapse warning to a select few people.
http://whatreallyhappened.com/oem_wtc.html

Fact: Giuliani was warned of the collapses.
http://whatreallyhappened.com/wtc_giuliani.html

Fact: Five Israelis danced as the twin towers burned.
http://www.whatreallyhappened.com/fiveisraelis.html

Fact: 600ºC+ fires did not exist in either of the twin towers.
http://whatreallyhappened.com/wtc_fire.htm

Fact: The core of WTC 1 failed below the third floor.
http://whatreallyhappened.com/wtc1_core_collapse.html

Fact: The BBC stated there were no casualties when WTC 7 collapsed. This is flat out wrong. Master Special Officer Craig Miller of the Secret Service died when the building came down.
http://whatreallyhappened.com/silverstein_pullit.html

Fact: An explosion was reported on Flight 93.
http://www.whatreallyhappened.com/shootdown.html

Fact: The Secret Service were not concerned about the safety of the President on 9/11.
http://whatreallyhappened.com/9-11secretservice.html

Fact: The President was in no hurry to get out of Booker Elementary School.
http://whatreallyhappened.com/schoolvideo.html

Fact: Eight minutes before the Pentagon crash Flight 77 was tracked by radar as it closed to within 30 miles of Washington, therefore the whereabouts of the plane was known, therefore it could have been intercepted.
http://whatreallyhappened.com/911stand.html

Fact: Dick Cheney left Washington undefended on 9/11.
http://whatreallyhappened.com/usaf_911.html

The BBC briefly mentioned that Flight 77 hit a reinforced section of the Pentagon. What they failed to mention is that reinforcements on this section were completed on 9/11/2001 meaning this section of the building was nearly deserted when the plane hit.
http://whatreallyhappened.com/911_pentagon_renovations.html

Fact: White House staff started taking Cipro on 9/11.
http://www.whatreallyhappened.com/frameup.html

Finally, why did the BBC report that WTC 7 had collapsed ~20 minutes before the event occurred?

The evidence doesn't support conspiracy theories?

Crap.

The evidence doesn't support the official version, and that is why this programme focussed on trivial issues.