Like everybody else, I have no idea what this is. I have, however, consumed scads of stories about military organizations encountering things they can't deal with. Some of these are quite prosaic for their situation, such as UN forces figuring out that the Chinese were entering the Koran War.
I _think_ I have enough of these examples to reach a tentative conclusion: for many organizations, the information that they've had incursions and are stumped is extremely important. If there's a known weakness, other competing powers might take advantage of it. What actually happened is besides the point. The mission is to control information, access to information, and the larger narrative.
You layer on half-remembered (and perhaps exaggerated) stories from fifty years ago and you get articles like this. My best guess is that this is very similar to what happened to the US Navy recently, only in this case the military has managed to confuse the issue enough that investigators will be debating details for decades to come.
Reality is not required to conform to our standards of scientific proof. If we can't observe or manipulate something, there's no way for us to scientifically reason about it. That's tough for a lot of folks to deal with.