I know, as an occasional Top Gear watcher, that Clarkson often likes to do some filming from a local pub. If that is the case, then 3 hours to do the filming would also go with the reports that he refused a selfie with one of the public in the hotel he was staying in. He said "Not with the kind of day I've just had".
Nobody keeps helicopters waiting like that unless they are extremely high business execs who have to sort something out. They are too expensive, run on too tight schedules and have to file flight plans which might be rejected depending on what is flying around above them.
Way too much of the reports I hear, but are not in the press, are very anti Clarkson. Even most of the press are anti Clarkson. Yet it was Clarkson who phoned his boss to report the "fracas". Let us not forget that.
Everything I've read so far points to a very rough day's filming which ran to high tempers, at the end of the day, because tired and grumpy presenters were offered minimal choice in food and a take it or leave it option.
The rest, I guess, will come out after the investigation by the BBC....