Couple of instances stand out for me.
I asked for access to the platforms at Bedford once. Initially asked for a platform ticket, but the clerk said "just ask at the barrier". The gateline operative let me through, but ordered me to sit on the bench just inside the gate where he could see me. Pointless as a vantage point for photos, so I left the station and went elsewhere.
Was stopped at Chester early one morning, having photographed the old signage and architecture on the old platform next to P1. Was told I could not take pictures of that area because it was a secure area. OWN GOAL! I did not know that was a secure area, but I do now, and so would a terrorist if he had been stopped.
I asked about taking photos at Paddington once and was told that I would have to have a safety briefing and wear PPE. "I order to stand in a public part of the station on the same piece of tarmac as I would if boarding the train I was photographing" I said. "Yes" he said, to which I said "Don't bother" and left.
Was challenged at Wokingham a couple of years back, for taking a photo of the new building. The member of staff started quoting all sorts of excuses, even when I produced the NR guidelines, saying that I needed written permission. When I took a trip to Weymouth a few weeks later, I (out of spite) wrote a letters to SWT asking for permission to take photographs at Basingstoke, Winchester, Southampton Central, Bournemouth and Weymouth stations.
Love the bit about challenging the "illegal" jobsworth with a magazine full of railway photos, will have to keep a copy of RAIL in my bag for the next time that happens!