There is a known issue with ffmpeg that apparently has yet to be fixed according their bug tracker. It looks like for now you will need to mux out the subs file from the mkv and play it as an external file or convert it.
For tools to add or replace subtitles from mkv files, as well as convert them to a subtitle format that doesn’t have embedded issues, check out this post => MKV files with embedded VTT subtitles can't be played
