I offered to help someone over on SpaceBattles with a crash in retail. Running the mission through a debug version of FS2_Open gives me this 
Assert: Ships[ship_index].objnum != -1
File: U:\src\cvs\fs2_open.testing\code\ship\Ship.cpp
Line: 11250
Call stack:
------------------------------------------------------------------
    mission_eval_arrivals()    mission_parse_eval_stuff()    game_simulation_frame()    game_frame()    game_do_frame()    game_do_state()    gameseq_process_events()    WinMainSub()    WinMain()    WinMainCRTStartup()    kernel32.dll 7c816d4f()
------------------------------------------------------------------
which makes me suspect that the mission is crashing cause there are too many ships in the mission. Am I right about that one?