Between Serbia and Croatia there are no trains running due do rail works in serbia. Best thing you can do is to take a bus (not included in Interrail) or to change your plan and go somewhere else. 

Maybe there are trains from skopje to belgrad and from there with the bus to Zagreb or the first station in Croatia Vinkovci to Zagreb (the bus is faster).

In the balkan area it is very difficult to get timetables. You could also think about to go by train to Montenegro Riviera like Bar and from there with an Bus (not included in Interrail) to Dubrovnik, Split and from Split back on rail. 

Or you could think about to go to Bulgaria, there are trains to Romania and from there to Vienna or Budapest. From Budapest you can go to Zagreb.