The detainees refused, however, to wear headphones so they could hear a simultaneous Arabic translation. To make sure they knew what was being asked, the judge directed translators to repeat in Arabic over a loudspeaker each phrase that was uttered in the courtroom, sometimes causing a confusing jumble and significantly slowing the process — especially after Mr. bin Attash insisted that prosecutors read the full charges, which consumed more than two hours.

The arraignment was the latest chapter for the detainees, who were captured and held for years in secret overseas prisons by the Central Intelligence Agency and subjected to harsh interrogation techniques. In 2008, they were charged before a tribunal and seen for the first time; Mr. Mohammed’s beard then was gray, and his behavior during pretrial motions was marked by frequent outbursts, not silence.

The high-security courtroom at this naval base was sealed; anything the detainees say is considered presumptively classified, and at one point censors cut off an audio feed when a defense lawyer said his client had been tortured, but later comments about torture were not. The sound also cut out at first when Mr. bin al Shibh began shouting — but was turned back on midway through.

Among the observers watching the proceeding behind soundproof glass were several family members of the nearly 3,000 people killed in the Sept. 11 attacks, separated from reporters and other observers by a blue curtain. (A closed-circuit feed was also broadcast to several locations around the United States.)

Several family members could be heard muttering when the lawyer for Mr. bin Attash, Cheryl Bormann — who wore traditional black Muslim garb, covering everything but her face — asked women on the prosecution team to consider dressing more modestly so that the defendants would not have to avoid looking at them “for fear of committing a sin under their faith.” The women were wearing military or civilian jackets and skirts.

Ms. Bormann later sought a court order preventing prison guards from forcibly extracting detainees from cells if they did not want to come to the next hearing, saying Mr. bin Attash had “scars on his arms”; as she spoke, he took off his shirts, but put them back on after the judge admonished him. Mr. Nevin also complained that Mr. Mohammed had been strip-searched that morning — which, along with not being allowed to wear the clothes their lawyers had brought for them, and not having a translation of the just-rewritten hearing script — had “inflamed the situation.”

Colonel Pohl said several such concerns were valid, but he would take them up at the next hearing.

Family members also whispered angrily about the disruptions. Against the backdrop of scrutiny over whether the military commissions system was a fair venue, Colonel Pohl appeared to be giving broader leeway to the defendants and the defense lawyers than many federal judges would tolerate.