Wow some of these comments are awful. You said he was only a minute or two late. Personally I would have thought this was acceptable if they said it was ok and he agreed to work those few minutes at lunchtime or after the usual finish time. I think most people would have taken the person at their word and if they said it was ok believed them. I guess that’s a lesson for next time - if something similar crops up - to get it in writing and for him to specifically get permission. As others have said, it might be that one person agreed but another person wasn’t happy and they’ve likely had a catch on”how’s he getting in?” whilst he’s been away. A more senior person has perhaps overruled the person who said it was ok.
Make sure he gets the right salary with his notice period etc although I guess he’s probably taken more holiday than he’s entitled to (but that’s just an unfortunate situation having booked a holiday and the timings of starting work).
I think it is really important in this to consider how many trains are running. If there’s a train 10 minutes earlier then he needed to catch that, but if it’s an hour earlier and he would have arrived 55 minute early most mornings then an agreement to be a minute or two late would be more reasonable perhaps. Maybe discuss this at the interview if he’s applying for jobs in the same city and likely to arrive a bit late. He should have agreed to work the missed time even if it’s a few minutes each day. If that didn’t fit in with trains, he could have asked about working the whole lost time on a single day or something. Best to get agreement at interview and discuss what happens if the train is late, or certainly on the first day of work.
As others have said, he/you probably cannot do much as they can get rid of anyone in their probation period for no real reason. I’m sorry he’s lost his job and I’d be annoyed too. I hope he gets sorted.
I’ve always worked at organisations where I have flexi time so I guess I don’t quite understand this. All my workplaces have been really flexible although I did do a part-time retail job in sixth form, got agreement to be late from the shop manager one day as I had an A level exam that finished late and I knew I’d struggle to get there in time, I rushed there after my exam, arrived 3-4 minutes late and was laid into by the area manager. I was only young and didn’t get a chance to even tell him I had permission to be late. I was so upset in floods of tears. Some managers can just be awful. In all my “proper” jobs including my current job (after the retail one), I could/can just turn up when I wanted as long as I work the core hours (10-12 and 2-4) and work the right number of hours per week / month. University, local authority and NHS jobs generally have flexible working. More difficult to get sacked for nothing too in the public sector!
Goox luck. Hope he gets sorted with a better job soon. Maybe take it as a blessing. It perhaps wasn’t the best place to work.