Perhaps your MIDI files contains duration = 0's note event. Though duration = 0's note isn't prohibited, but if note on time and note off time is same, maybe it cause corrupution when editing such as moving note, So in Sekaiju, for the safety, duration >= 1 is recommmend.
To find which note is, please use SAL (Sekaiju Application Language) which is provided external extension program. SAL can be used for free trial while 30 days.
Following script is to detect duration <= 0's note in all selected event.