I believe you are quoting Wikipedia.
It is impossible to say with any certainty what this incident might represent. It is long ago and a proper investigation would be required, both interviewing all witnesses and testing the relevant equipment (hardly likely given that is mostly military) that showed abnormal function.
However, it is possible to comment on such cases in general.
Firstly, anomaly reports (including UFOs) are usually generated by a coincidence - several factors that rarely come together. So, for instance, some aspects of the incident, like unusual radar echoes, could be unrelated to the sighting itself. Also the various different objects reported may have been unrelated but given high significance by virtue of the main report.
Secondly, once an interpretation has been made at the time, people tend to look for confirming factors, rather than confounding ones. In other words, evidence that the event had a natural cause might have been overlooked or misinterpreted.
Thirdly, witness 'credibility' is not a useful factor to bolster any case. Though some people may be better observers than others, everyone can and does misperceive.
Loking specifically at the Wikipedia account, several points are interesting. Descriptions of the initial object from the ground vary, as do those from the air.
The follow up: "The next day, the F-4 crew flew out in a helicopter to the site where they had seen the smaller object land. In the daylight, it was determined to be a dry lake bed, but no traces could be seen. They then circled the area to the west and picked up a noticeable "beeper" signal. The signal was loudest near a small house, so they landed and questioned the occupants of the house about any unusual events of the previous night. They reported a loud noise and a bright light like lightning."
This looks like a classic case of 'look and you shall find'. I've little doubt they'd have found something interesting if they'd gone to completely the wrong place. Maybe the loud noise and lightning were - nearby lightning!
The differing descriptions of the main object point to some sort of misperception, perhaps of an unusual atmospheric event. We certainly do not know everything about our atmosphere. For instance, sprites were only discovered very recently, despite being massive phenomena. Maybe something similar can happen at lower levels in the atmosphere sometimes. This is just speculation. As I say, it would need to be investigated properly. Those UFO cases that HAVE been investigated properly have always yielded at least the certain possibility of natural causes.