Maybe something from what Gallagher saw and didn't see, made him assume the plane sank at sea.
He was told it was not AE after they examined the bones. Then after reading files on the subject later he wrote:
"It does look as if the skeleton was that of some unfortunate native castaway and the sextant box and other curious articles found nearby the remains are quite possibly a few of his precious possessions which he managed to save."
"managed to save" sugggests to me he was thinking the castaway did not have time to salvage much and that the castaway came from a sinking vessel. When he thought it may be AE, he may have thought the sinking vessel was a sinking plane. So maybe he never thought to do any more searching for a plane than what was already done in the area for other items.
Since he was told the bones were not AE, he may have told the colonist the same. So if colonist saw plane wreckage after the bones were found, then they could have thought it was a different plane.
Now if colonist saw plane wreckage before the bones were found and before Gallagher died, another possibility could be Gallagher investigated and found what they saw was not aircraft wreckage. A mix up as to location of what was seen and what was investigated could cause this.
Also if some wreckage was tied to the edge of the reef. (in an attempt by AE to save the plane), it could have been playing paddle ball and hide and seek. Some days its on the reef, and some days over the edge and not vissible. It keeps getting washed on and off but stays tied down in the area for months
Maybe Gallagher sees nothing and tells the colonist they probably saw NC stuff, even though they still see wreckage later. Somehow the mix of stories and who saw what, and when, the wreckage playing hide and seek, leaves a paradox