Seat reservations for short train ride- sold out. Can we board and stand on the train?

What train exactly?

Most likely this is again one of the many errors of the app/site. Try first bahn.com-its a generally far better planner and shows clearly if a train should be REServed -or not, and even if its mandatory or optional.

I ask which train  as there are a few odd trains that are in fact kind of holidaymakers trains to the coast/Split and for which you have to accept that with a pass there is a very high surcharge-to discourage such trips.

And check train earlierlater-there are also a few local trains on this line.

Have you ever been on trains? Have you ever even encountered there is NO check-in, no boarding pass, NO airline style access-anyone just gets on-and tries to find allocated or other seat-or stand. IN general in Hrvatska it also works like that-as about anywhere in EUR-except the tipical hi-speed trains with gated access in FR/ES/IT.

I would walk from Dobova to Harmica, it is a walk of 30 minutes and from there, you can go every hour to Zagreb without a reservation.

Depending on the time of day I suppose… the OP didn't specify which train(s) or a departure time.