The CTs are suspicious of the 9/11 Commission report for several reasons:
1. Testimony of certain individuals is omitted (Edmonds, Rodriguez)
2. The report does not address WTC 7
3. The report contradicts other evidenciary sources on matters of fact (Otis fighter timeline)
4. Other matters have come to light since the report was released that cast doubt on its comprehensiveness (Able Danger)
5. The report is rather gentle in its political conclusions (it largely lets both Clinton and Bush off the hook, politically)
I think these are fair criticisms. I don't conclude from these, however, that 9/11 was a false flag op carried out by the government. I tend to conclude from all of this that internal political considerations played a big part and there was certainly a lot of ass-covering/incompetence/negligence going on, particulary in the case of the FBI (Edmonds).
That said, I think it's a mistake to dismiss the entire report, esp. as it is so well-sourced. In fact, the sourcing is what has made the inconsistencies so easy to find. I think the report could benefit from a revision to address/cleanup some of the contradictions, and to look at some of the things that have (rightly, IMO) been brought up since -- namely, Able Danger and Sibel Edmonds. I hope the Commission members will do that at some point.
Also, I think a lot of the criticism deals with facts around the "edges" of the story -- issues of who knew what when and were people doing the jobs they were supposed to be doing. None of that really undermines the basic truth that 19 jihadists hijacked some planes and flew them into some buildings (or the ground in PA) on 9/11.
Edit: typo