The story...

On September 20th and 27th, Mueller admitted on CNN that there is "no legal proof to prove the identities of the hijackers"
Loose Change

Our take...

There’s no doubt that the FBI expressed considerably uncertainty, early in the investigation. Here’s a BBC quote from around the same time:

21st September 2001
The FBI has said that the identities of some of its list of 19 hijackers behind last week's devastating attacks are in doubt.
http://news.bbc.co.uk/1/hi/world/americas/1553754.stm

But then again, that was only ten days after the attack. After reporting that they had investigated the questions that had been raised, the FBI also announced in November 2001 that all doubts had been resolved.

The FBI has resolved questions about the identities of the 19 hijackers involved in the Sept. 11 attacks and has discovered places outside the United States where the conspiracy was planned, FBI Director Robert Mueller said Friday.

Saudi Arabian officials and others have questioned whether some of the hijackers identified by the FBI in the weeks after the attacks used stolen identifications. Mueller said those questions have been answered.

"We at this point definitely know the 19 hijackers who were responsible," he said.
http://www.cbsnews.com/stories/2001/11/02/attack/main316806.shtml

Of course we can’t prove that Mueller really believed that, however the point is clear: the first quote is long out of date, and people or sites who still use it, without mentioning what they said next, are not telling the whole story.