I don't think it's an automation-related thing. It happens even on big name shows on big apps.

I think it's a toolkit thing where some sort of event or timer goes off at the wrong time and the subtitles get cleared when they shouldn't. And then if you rewind and replay, it doesn't happen again (because spurious event/timer issue).

At least with vtt and srt, the chunk of text displayed is explicitly associated with a chunk of time, so something like that really shouldn't be happening. Maybe there is some sort of subtitle-writing on the fly like what is sometimes done with transcoding video, but that would be really strange for a plaintext format that is so light compared to the video and audio coming with it.