As of now (24 Sep 2015) all international railway connections are suspended between Croatia and Hungary, Serbia and Slovenia
Details at: http://www.mavcsoport.hu/havaria/international-traffic-restarted-towards-austria-suspended-croatia
http://www.slo-zeleznice.si/sl/novice/potniski-promet-novice/prekinjen-potniski-promet-med-slovenijo-in-hrvasko (in Slovenian, use Google Translate for English)
http://www.hzpp.hr/obustavljen-zeljeznicki-promet-prema-sloveniji-ma%C4%91arskoj-i-srbiji (in Croatian, use Google Translate for English)
Slovenian railways provides replacement shuttle bus services in some lines (like part of the Ljubljana-Zagreb line)
Ask them before departing about details
From Hungary to Croatia and Croatia to Hungary the Eurolines international bus services are recommended.
Web page: www.eurolines.hu
Check the current situation before departure as the situation changes very fast.