It is not illegal to take pictures or videos of trains. using the "well since 9/11" is getting old fast. Just cause some rent a cop doesn't like it does not give them the right to abuse there power and go on a ego trip. You also got paranoid engineers who report railfans more and more these days.
Yes, that happens. Sometimes operating personnel do so because they themselves were doing something contrary to regulations which got recorded in your photo. We (several of us from this board) were involved in an incident at an LIRR station where an LIRR train showed up with the rear flag riding in the front cab. As we proceeded to take photos she first said we were interfering in her work, which we pointed out could not be true. Then she came off the train, and we pointed out she was now trying to interfere in our freedom, upon which she went back and called the cops. The cops ignored her and did not show up. I suspect her main concern was that she was recorded being present at a place in the train where she was not supposed to be according regulations.
A few engineer acquaintances at NJT tell me that they try to avoid calling cops unless they want to be stuck passing that spot where they called from at reduced speed until the cops take their own sweet time to complete their investigation.
But then again, if the photographer is indeed doing something wrong, like infringing on the RoW, then rightfully they should be reported, because they are a potential danger to themselves and others at that point.