There are several things that I guess have always bothered me.
First the plane that crashed in PA. While there was a lot of evidence that has been released in regards to cell phone calls, and there's the whole tragic story of the heroic takeover of the plane that sadly failed to actually recover the plane, I can't shake this idea that it was actually shot down. I remember hearing early reports stating that it had been shot down (which is completely understandable considering the circumstances) then it started becoming the story that became a centerpiece of patriotism that became a battle cry. It has always settled weird with me, right from the notion of the cell phones working on the plane, all the way to how I never heard anything else discrediting that live report I heard that it was shot down. In this case, the motives behind fabricating a story seem clear. I could see the reasoning behind why they would possibly think it necessary to protect the public from the idea that we shot down a plane of innocent civilians, but I also think most of America would have understood why we did it since we had two planes fly into the wtc, and a plane in the pentagon. A split decision was required. This would also explain the lack of wreckage (although a nose dive might be possible too but I have absolutely no expertise in this stuff). However, if it the story was made up, I find it despicable that it was used as nothing more than a propaganda piece.
Second, the neatness of the collapse of the towers. This has always bothered me. I would understand the heat and/or impact causing the towers to topple over on itself, but the way both towers collapsed just like you see with a controlled demolition has always been something I've wondered about. Then tower 7 going down, again in a neat stacked collapse. It all makes me wonder why they put in so much effort to demo a building if this is how they collapse anyway. Although to be fair, I thought I read somewhere a long time ago that they chose to demo tower 7 because it was compromised, although the fact it happened so quickly made me wonder how they made the decision and got it set up for demo so quickly. I recently saw this clip, and it has kind of confirmed some of my suspicions (yes it has the cheesy conspiracy music) but I found some of it compelling.
Now, I'm still not sure why, or who would orchestrate such a thing. It's possible the terrorists had a ground crew. It's also possible that it was our government, but I'm not sure why. The military industrial complex and it's influence over our government (and the then current administration) comes to mind, but I'm totally speculating. Beyond that I really have no idea why.