The New York Times reports:

The euphoria that followed the rebels’ triumphant march in Tripoli gave way to confusion and wariness on Monday, as Col. Muammar el-Qaddafi remained at large, his son Seif al-Islam made a surprise appearance at a hotel with foreign journalists, and pockets of loyalist forces stubbornly resisted rebel efforts to take control of the capital.

While rebel leaders professed to be making progress in securing Tripoli and planning for a post-Qaddafi government, and international leaders hailed the beginnings of a new era in Libya, the immediate aftermath of the lightning invasion was a vacuum of power, with no cohesive rebel government in place and remnants of the Qaddafi government still in evidence.

Seif Qaddafi, who was brandished as a trophy capture by the rebels on Sunday and through much of Monday, presented himself to foreign journalists confined to the Qaddafi-controlled luxury Rixos Hotel in the center of Tripoli early Tuesday, boasting that his father’s government was still “in control” and had lured the rebels into a trap, the BBC and news services reported. His appearance raised significant questions about the credibility of rebel leaders.

It was not clear whether he had been in rebel custody and escaped, or was never held at all. Another Qaddafi son, Muhammed, escaped from house arrest on Monday.

Fighters hostile to the rebels still battled on the streets and rooftops of Tripoli, injuring or killing at least a dozen people. And Colonel Qaddafi’s green flag still flew in parts of Tripoli and over at least two major cities considered strongholds of his tribe, Sabha to the south and Surt on the coast roughly midway between Tripoli and Benghazi. The Pentagon reported late Monday that its warplanes had shot down a Scud missile fired from Surt.

Reuters adds:

Saif told journalists that Tripoli, which has been largely overrun in the past 24 hours by rebel forces seeking to topple his father, was in fact in government hands and that Muammar Gaddafi was safe.

Earlier, armed pro-Gaddafi security men guarding the hotel took a small group of journalists to Gaddafi’s Bab al Aziziyah compound, where they had a meeting with Saif.

They returned to the hotel accompanied by Saif, who then spoke to journalists in the lobby before taking some of them back to the compound a short distance away for a brief visit.