According to Defenselink.mil the FBI only spent 5 days working the crime scene at the Pentagon.
http://www.defenselink.mil/news/newsarticle.aspx?id=44840
WASHINGTON, Sept. 24, 2001 –
The FBI assumed crime-scene jurisdiction at the Pentagon terrorist attack site Sept. 21 from the Arlington County (Va.) Fire Department, officials said.
FBI officials estimate the crime scene investigation would last about a month, Arlington Fire Chief Edward P. Plaugher said. He said he expects "additional remains will be discovered during the course of the FBI investigation" and mortuary specialists will remain on site to process them.
http://www.defenselink.mil/news/Sep2001/n0..._200109266.html
WASHINGTON,
Sept. 26, 2001 -- The FBI handed over Pentagon crash site management to the Army Military District of Washington at 7 a.m. today.
The transfer of responsibility marks the end of the FBI's crime scene investigation following the Sept. 11 terrorist attack against the Pentagon. MDW will oversee ongoing security operations around the damaged area of the building. FBI investigators will move their operations to the Pentagon's north parking lot and continue to sift through debris for more evidence.