To answer the original question, as I understand it. All aspects that cause someone to question events in the main conspiracy theories have been explained by reputable sources.
Without starting another debate, one on my favourites over the years is the moon landings. Now all the so called anomolies have been explained ad infinitum, yet there are people who choose to ignore the explanations and persist with the movie theory. In fact the conspiracy theorists hatch ever more complex ideas on how a partictular effect was acheived to the point where it would actually be easier to go to the moon! and hence debunk their own theory. For example we where told how NASA could have faked the moon rocks, and the BBC Horizon program decided to try and fake some moon rocks. At the end of the program they concluded that it would be easier to go to the moon to get them!