From the Sunday Times Online (UK):

The capture of a supposed Al-Qaeda kingpin by Pakistani agents last week was hailed by President George W Bush as “a critical victory in the war on terror”.  According to European intelligence experts, however, Abu Faraj al-Libbi was not the terrorists’ third in command, as claimed, but a middle-ranker derided by one source as “among the flotsam and jetsam” of the organisation.

[…] Another Libyan is on the FBI list — Anas al-Liby, who is wanted over the 1998 East African embassy bombings — and some believe the Americans may have initially confused the two. When The Sunday Times contacted a senior FBI counter-terrorism official for information about the importance of the detained man, he sent material on al-Liby, the wrong man.

“Al-Libbi is just a ‘middle-level’ leader,” said Jean-Charles Brisard, a French intelligence investigator and leading expert on terrorism finance. “Pakistan and US authorities have completely overestimated his role and importance. He was never more than a regional facilitator between Al-Qaeda and local Pakistani Islamic groups” [emphasis added]

(via Hal the Hellblazer)

For what it’s worth, the Sunday Telegraph (UK) has a different take, and in a cursory search I haven’t been able to find any other news sources supporting the Times‘ assertion.

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update: Robin points me to Dan Darling’s more thorough analysis at Winds of Change; Dan argues that this is not a case of mistaken identity—though he also disputes the number 3 designation touted by the U.S. government.