Train from Budapest to Ljubljana.

That train runs every day. Do you need a reservation? If you buy it in advance (2 weeks would be enough), it might cost you as little as 25€. If you buy it on the day and at the station you might pay twice that. Then you will need to buy a seat reservation which I think will be 2€. Buying in advance you get more seat choices. On the day of the train, you buy what they have and try and communicate your choice to the one selling the tickets. Thos tickets won’t go on sale until maybe June.

The MAV ticket site. Some report issues. I use it often and haven’t had the same issues. I have used it with local and US IP addresses with the same relative ease. But I use the Website and not the App. https://jegy.mav.hu/ The App did have issues and I haven’t tested it to see if they have been resolved. If you do have issues, then I presume you will be here in Budapest a few days prior to the trip to Zagreb, use your phone and the hotel WiFi and you will be using the exact equivalent that I use with no issues. If you are concerned, then write me and together we overcome them. No problem.

The bus as a backup? Sure, keep their website, but you wont need it. The train will indeed run.

Next question is more about your trip planning. If you are going from Zagreb south through Croatia, then consider going the other direction. Then you can take a direct flight to Dubrovnik or Podgorica. That takes about 1:15 and costs under $50 with a carryon and maybe under $75 with a checked bag. Personally, I would start in Podgorica and head north. I enjoy Montenegro a bit more than Croatia. But its all preference, you cant do wrong.

If it’s an environmental concern. I get that too. But in September, you may find yourself one of 50 on a train with a capacity of 200 vs a full flight. Not sure of the carbon footprint difference in that situation.