Part and parcel of the moment of collection is the sample's in situ description and relevance to the event being documented (e.g., an oil spill). If I were to collect a soil sample for analytical oil and grease (O&G) analysis, the date, time, and physical conditions (e.g., visual and olfactory descriptors) should be noted on the custody form. This is essentially Step One in starting a valid chain of custody.
But it is possible to have a valid chain of custody AND improper sample collection. Using the above example, I could submit a soil sample for O&G analysis following an underground storage tank leak. But if I collected the sample from the top of the pit as opposed to the bottom where there a sheen atop the groundwater is observed and notable volatile organic odors are present, my expectation is that the bottom sample would result in a higher O&G concentration than the top. Thus, there is a difference as to "where" the sample is collected, although both can be construed as having been collected "at the site" one is clearly more relevant.
Similarly, if I collect a sample - say of WTC dust - that had been gathered by untrained persons cleaning their New York City apartment a number of days after the collapses and using unknown cleaning tools, placing the dust into an unsecured plastic baggie who's origin (e.g., used or new) is unknown, storing the dust in an unsecured box for a cross-country move, and finally unloading the box and sample in California, and storing it for a number of months in an unsecured collection with no chain of custody to prove that what was detailed actually happened, then what should my expectation be of the sample – if I collect a portion or aliquot of the dust from the plastic baggie and initiate a valid chain of custody?
What should my expectations be if a sample of affected metal was collected months later from an original WTC structural member, but the structural member had been relocated hundreds of miles away from "Ground Zero" and incorporated into a larger water effects monument? Well, there's very little useful inference that can be drawn from such a sample because the other metal in the monument and its associated assembly process could contaminate the original WTC structural member. Weather effects from being exposed for such a long time prior to sample collection will impact what the member was actually "like" at the time of collapse. The presence of water nearby and/or atop the member's surface will certainly chain the ratio of substances found on the surface of the member.
In the end, you can only report that the analytical results are from a WTC structural member that has undergone extensive changes since its discovery at Ground Zero. Therefore, the results are not indicative of the actual conditions at the time of collapse.
Now, would you regard these samples as being representative of the conditions that existed at the WTC complex and surrounding area immediately following the structures' collapses? If you do, then you would (by logic) be open to reviewing the results of other samples as being more relevant given that their respective dates/times were closer to the actual collapses and were in situ at he time of collection. And such samples do exist – at numbers well beyond the two thus far that Dr. Jones has reviewed - http://pubs.usgs.gov/of/2001/ofr-01-0429/sample.location.html .
The end result is that you should trust your common sense rather than those opposed to any sense in this matter.