I have a file that has 4 subtitle tracks that are longer than the video track. The video plays fine but the length is wrong. It sounds like a similar problem to this: https://help.mkvtoolnix.download/t/strange-long-unclickable-dead-zone-at-the-end-of-mkv-file-see-explanation/514
But I’ve tried using the “Stop after video track ends” option and it doesn’t cut the tracks, the output file is identical.
I think “Stop after video track ends” only checks the start timestamp of the subtitle event, not the end timestamp. So if the last subtitle event starts before the video ends but lasts until after the video ends, this feature will not help you. You will have to edit the end timestamp of the last subtitle entry or remove that entry completely from the subtitle track with some other software (eg. “Subtitle Edit”).