The story...

Fluorine at the WTC is a key marker of thermite. Or, as Professor Steven Jones puts it:

We find in the previously-molten metal samples significant concentrations of FLUORINE and other unusual elements (data shown later in this presentation). Fluorine is a fairly common fingerprint in thermite mixtures, as we shall see. Does Greening (or anyone else) have an explanation (other than thermite-mixtures) for the presence of Fluorine? We have not found any explanation other than THERMITE mixtures, which accounts for the Fluorine and ALL the rest of the observed data (hightemp. sulfidation, large pools and flowing metal, etc.)
http://worldtradecentertruth.com/JonesAnswersQuestionsWorldTradeCenter.pdf

Our take...

Professor Jones further explains his position here:

Fluorine is present in an oxidizer using Polytetrafluoroethylene as its base, used in thermite charges.
http://www.osti.gov/bridge/servlets/purl/1344-QDsu9M/webviewable/1344.pdf

• Potassium Permanganate (KMnO4) is also commonly used as an oxidizer in thermite-reactants (aluminothermics).
• Hence, K, Mn and F are often present in thermite residue, suggesting they are part of a “thermite fingerprint” at WTC.
http://worldtradecentertruth.com/JonesAnswersQuestionsWorldTradeCenter.pdf

And he quotes another document to justify picking on elements like fluorine and manganese as a signature of thermite:

“When thermite reaction compounds are used to ignite a fire, they produce a characteristic burn pattern and leave behind evidence. These compounds are rather unique in their chemical composition, containing common elements such as copper, iron, calcium, silicon and aluminum, but also contain more unusual elements, such as vanadium, titanium, tin, fluorine and manganese. While some of these elements are consumed in the fire, many are also left behind in the residue.”
http://www.materials-engr.com/ns96.html

What he doesn’t do is attempt to discuss other sources, leaving it as an open question for others. So might there be an answer?

One option may simply be to consider Professor Jones’ own suggestion, Polytetrafluoroethylene. You might know this better as PTFE, although there’s a more famous brand name, and other possible applications:

Teflon and other nonstick coatings are actually a fancy sort of plastic called polytetrafluoroethylene, or PTFE. This plastic is also used to make fire-resistant cables for linking phones and computers when the wires are run through the space above the ceiling tiles. A thin white tape made of this plastic is often used to wrap around threads of plumbing to seal joints. And it is used to produce Gore-Tex and other waterproof, breathable membranes.
Source

Can we really be sure that the most likely form of PTFE at Ground Zero would be in the form of a base for “thermite charges”?

Further, fluorine is also used in compounds like Freon:

Trademark for any of several organic compounds containing fluorine (fluorocarbons) and sometimes chlorine (chlorofluorocarbons, or CFCs). Nonflammable, nontoxic, and noncorrosive, they have low boiling points, which makes them useful as refrigerants. By the mid-1970s they were in wide use in refrigeration and air conditioning systems, as blowing agents for plastic foams, as fire-extinguishing agents, and in aerosol sprays. Evidence has accumulated that decomposition of CFCs in the stratosphere destroys ozone there (see ozone layer), so most of their uses have been banned. International agreements signed by most of the industrialized countries have called for the phasing out of CFC use.
http://www.answers.com/topic/freon

And Freon was particularly relevant at the WTC:

Huge underground tanks held more than 200,000 pounds of Freon stored to cool the seven buildings of the WTC complex. This had been the largest air-conditioning system in the country.

OSHA personnel were concerned that workers entering areas below grade could be exposed to Freon gas, a known, heavier-than-air, invisible killer. After a leaking tank was discovered, agency staff and the site construction manager carried out special sampling for months until all the tanks were uncovered and safely removed.
http://www.osha.gov/Publications/WTC/dangerous_worksite.html

It’s our understanding that Freon was never a danger at the site, which suggests leaks were minimal. And perhaps it’s entirely impossible for a Freon leak to produce fluorine traces on WTC metal samples, anyway (don’t look to us for in-depth knowledge of chemistry). But if this, other refrigerants or plastics might have been responsible for the fluorine discovered by Professor Jones, then maybe we don’t need to invoke thermite charges to explain them, after all.