Zagreb - Ljubljana
 

Looked on both Croatian rail site and Sloven rail site and can find no way to book this. Going to be there in June/July and like having everything lined up and ready...any help or a site to book would be a big help

Rail Europe site wanted like 70$ when I looked while Sloven rail site said something like 20 Euros

None of these trains require reservations, so booking ahead is not going to gain you anything. (The Internet age seems to have conditioned us all into always wanting to do everything online and in advance, whether we need to or not... but in this case I really see no point)

I did this trip in the spring of 2014 and I am fairly certain that it wasn't possible to buy a ticket online.I bought the ticket at the station, probably a day or two beforehand.
It's a very nice train ride.

The usually reliable Man in Seat 61 currently says that it's not possible to buy the ticket online, so that's probably still the case.