Lotfi Raissi (right) denies involvement in the 11 September attacks
Algerian Lotfi Raissi, 27, appeared at high security Belmarsh Magistrates Court in south-east London on charges of making a false statement when he applied for a US pilots licence.
But US prosecutors have made it clear this, and 11 similar counts to be brought later on Tuesday, are "holding charges".
Two other men have also appeared in court facing separate extradition proceedings.
Pentagon
Mustapha Labsi, 32, is wanted in France over an alleged bomb plot targeting the G7 summit in Lille five years ago.
And London-based Amar Makhlulif, 37 is accused by the US of involvement in an alleged millennium eve plot to blow up an airport in Los Angeles.
All three men were remanded in custody to 14 December.
US prosecutors believe Mr Raissi was a "lead instructor" for the man who took control of the flight which crashed into the Pentagon - but the FBI says it is still gathering evidence on these allegations.
Tuesday's extradition proceedings were brought on a charge of making a false statement on a US Federal Aviation Authority application.
'Innocent'
Lawyers said 11 further charges of falsifying immigration forms would be presented in the US later on Tuesday.
Mr Raissi's lawyer said his client was innocent and it was a disgrace that after two months no substantial evidence had been produced.
Metropolitan Police officers arrested Mr Raissi, who was living at Colnbrook, Berkshire, near Heathrow Airport, on 21 September.
He denies any involvement in the US atrocities.
High Court ruling
Mr Makhlulif, who was arrested in July, is charged with conspiracy to cause explosions.
He is accused of helping terrorists travel to Bin Laden's training camps in Afghanistan and of sending others to Canada to prepare for the attack.
There was no application for bail and he was remanded in custody.
Both Mr Makhlulif, also known by the surname Doha, and Mr Labsi have been named by prosecutors in the US in connection with the alleged LA airport bomb plot.
Last week the pair won an important human rights ruling which opens up a new possibility to resist extradition for those accused of being involved in foreign crimes.
Two High Court judges ruled that in future, magistrates - and not the home secretary - will initially decide whether extradition proceedings are tainted by certain types of "abuse of process".