Subtitles of mkv and webm files are displayed incorrectly

I downloaded several videos from Youtube using youtube-dl and embedded auto-generated subtitles. If the output format is mp4 then subtitles are displayed regularly, but if it's mkv or webm every string of subtitles begins with align:start position:0% and shows timestamps on screen (the actual content of the .vtt file). I also tested all the videos with mpv to exclude the embedding process as the issue, mpv displays subtitles correctly for every format. If it were simply a problem of the additional text in the .vtt file for the auto-generated subs, mp4 files too would be displayed incorrectly, but this is not the case.