There are a number of publications and websites that address the bulk of the conspiracy theory elements point by point. Those who want to believe in a conspiracy tend to claim “they’re in on it”, are “co-conspirators”, “do the government’s work” and are “traitors”. The problem with that broad brush is that it’s not an argument, unlike the material put forth by those supposed traitors.
There are two basic approaches to gaining knowledge.
1) you start with a favored assumption and gather supporting evidence to the exclusion of material that contradicts it.
2) you investigate an incident, prioritizing scenarios according to how (un)likely they are, progressing from simple explanations to more intricate ones only when the simple ones no longer suffice to explain the facts. In that process lots of ideas get tossed out as unsupported.
Somehow, that tossing out never seems to happen in the case of the conspiracy crowd, they never care to check, and stuff that has been shown to be utter nonsense still circulates as ‘new research’.
That said, it’s no secret that the gov’t tried to hamper the investigation where it would have shown its failures leading up to the attack and its in part poor handling of the situation afterward.