I was out of money buying a lot of things and tried to use the [highlight=blue]Subway in Kanto and it worked without money[/highlight], i was with 800$ and it worked free.
I tested it in Johto but the NPC said i had no money so in [highlight=blue]Johto is working but in Kanto is bugged[/highlight].
I have not tested with the Kanto-Johto travel because I had the (100.000$ ticket free for 1 week or something like that) so it was free as expected.
(Subway costs 2,500$ every travel from Pokecenter to Pokecenter)