For once I would like to see a newspaper reporter write a report on this type of crash and make it understandable. This most recent link mentions an eyewitness couple stating that they did not see the flashers and gates working. However, the article simply does not make clear how they encountered the crash.
If I had to guess what the newspaper report means, I would say the Vaughn couple did not witness the impact, but rather, arrived at the crash crossing a minute or two after the impact, by which time the train would have been stopped a half mile or so down the track. By that time, people had gotten out of their cars and were looking around the scene, even though the train and the car were gone.
The Vaughn couple did not observe the flashers and gates working, but with no train present, there was no reason for them to be working. Nevertheless, when they went to the crossing where the train stopped, they must have explained to rail workers there that they had just come from the crossing where the crash occurred. Then the rail workers asked the couple if they had seen the flashers and gates working, and the Vaughn couple accurately said that they had not. Apparently, it has not occurred to them that their failure to witness flashing lights and lowered gates is being misrepresented and/or misinterpreted as meaning that there was a malfunction of the crossing warning system.
Also, apparently, it has not occurred to the newspaper that they are making this misinterpretation of what the Vaughn couple said.