When the cargo bays of the DC-8 were full, an interesting situation arose; there were still 41 of the soldiers' duffel bags that could not be loaded. Many of the bags were bumped off the plane due to several "large, wooden crates" that were loaded onto the plane first. (7:182) An Arrow Air manager recalled that Lieut. Colonel Marvin Jeffcoat, the battalion commander, insisted that the boxes be loaded first, and if necessary, that duffel bags be removed to accommodate the boxes, as they contained "very important, military material." (2:146) This struck many of the crew members oddly since it is "unusual to separate a soldier from his equipment." One of the 10 to 20 of these crates had not been transported on the baggage truck with the other baggage and boxes, but had been flown in the belly of one of the 737s to Cairo. (2:147) Where was this box kept while the other baggage in the trucks was being guarded? Despite attempts to identify the contents of these boxes through Army records, no official records of the boxes, or their contents, have been found.

Two separate eyewitnesses remember General Crosby ordering the "immediate bulldozing of the crash site." Although General Crosby denies mentioning the bulldozing operation in December, records show that less than 10 days following the accident, Crosby was in touch with officials in Gander and Ottawa regarding the site cleanup, which was to be performed with "a representative of the Army present at all times." (2:83-85) The immediate bulldozing of a crash site removes all traces of wrongdoing, and seems especially intriguing in light of the Pan Am 103 investigation which took place after that flight was brought down by an explosion over Lockerbie, Scotland. Investigators in the Pan Am case reconstructed the aircraft piece by piece until the source of the explosion was found: a detonator small enough to fit in the lock of a suitcase was found among the 747's wreckage. (2:431) No meticulous investigation such as this was made in the Gander accident. The bodies of the deceased were the only hard evidence examined for an in-flight explosion, and even they were hurriedly examined.

Dr. David Elcombe, director of the Canadian Aviation Safety Board (CASB), released the Canadians' toxicological findings on March 5, 1986, although they were not presented at any public hearings. These results presented problems for the "instantaneous" death theory posed by Dr. McMeekin. The consensus between the two governments was that there was no pre-impact explosion. Therefore the story went something like this: everyone was alive, then several seconds later, all aboard perished immediately when the plane contacted the ground as a result of wing icing, and erupted in a ball of fire. This is where Dr. Elcombe's findings pose a problem. Many of the bodies contained high levels of carbon monoxide and hydrogen cyanide, both products of combustion. (1:37-38) An accepted guideline used by pathologists is that these products cannot enter the tissue of the body by any means other than respiration. So according to Dr. Elcombe, 256 people who died "instantaneously" have high levels of combustion products which they would have had to have inhaled. To make this important piece of evidence fit into the accepted "no explosion" theory, the survival time after the crash was increased from zero seconds to almost five minutes. The families were being asked to deal with the nightmarish possibility that their loved ones sat living, within a fiery inferno of jet fuel for almost five minutes. Interestingly, many of the bodies that had high levels of combustion products in their lungs were also decapitated, yet according to the official report, they somehow kept breathing five minutes after being dismembered. This could be exactly why Dr. Elcombe sent a memo to Dr. McMeekin dated June 20, 1986 stating: "Some of the carbon monoxide and hydrogen cyanide values are striking ... and I look forward to meeting with you ... to consider their significance." (2:167)