For LIRR I select explore on foot, location Hunterpoint Avenue. First time, I was ported to Garden City, the second time to Hillside. This clearly is a bug.
Let's do it empirically: 1) A restart does help very very rarely, but at least you don't have to go back to the main menu. 2) I did 64 attempts before I got to Hunterspoint a second time. Lots of other stations I've seen up to 4 four times, but some even never. 3) There's no specifical order, it's completely random. 4) The time of day doesn't seem to have any influence.