It seems that there is a bug when generating the muxer headers when an EOS is received and not media has been processed previously.

You can try this issue with gst-launch:
$GST_DEBUG=2 gst-launch-1.0 videotestsrc num-buffers=0 ! x264enc ! .video_0 matroskamux ! filesink sync=FALSE async=FALSE location="file.mkv"

0:00:00.032486501 30736      0x24c3370 WARN             matroskamux matroska-mux.c:3333:gst_matroska_mux_finish:0x24c4a00 unable to get final track duration

The resulting file.mkv is a not playable file:
$gst-play-1.5 file.mkv 
Press 'k' to see a list of keyboard shortcuts.
Now playing /home/sancane/twilio/sources/vms-media-server/build/file.mkv
0:00:00.026630030 30784 0x7fae40130990 ERROR               ebmlread ebml-read.c:152:gst_ebml_peek_id_length:<matroskademux0> Invalid EBML ID size tag (0x0) at position 244 (0xf4)
0:00:00.026777265 30784 0x7fae40130990 ERROR              decodebin gstdecodebin2.c:3069:no_more_pads_cb:<decodebin0> can't find group for element

ffprobe gives next info:
$ ffprobe file.mkv 
ffprobe version 2.8.10-0ubuntu0.16.04.1 Copyright (c) 2007-2016 the FFmpeg developers
  built with gcc 5.4.0 (Ubuntu 5.4.0-6ubuntu1~16.04.4) 20160609
  configuration: --prefix=/usr --extra-version=0ubuntu0.16.04.1 --build-suffix=-ffmpeg --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --cc=cc --cxx=g++ --enable-gpl --enable-shared --disable-stripping --disable-decoder=libopenjpeg --disable-decoder=libschroedinger --enable-avresample --enable-avisynth --enable-gnutls --enable-ladspa --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libmodplug --enable-libmp3lame --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-librtmp --enable-libschroedinger --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265 --enable-libxvid --enable-libzvbi --enable-openal --enable-opengl --enable-x11grab --enable-libdc1394 --enable-libiec61883 --enable-libzmq --enable-frei0r --enable-libx264 --enable-libopencv
  libavutil      54. 31.100 / 54. 31.100
  libavcodec     56. 60.100 / 56. 60.100
  libavformat    56. 40.101 / 56. 40.101
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5. 40.101 /  5. 40.101
  libavresample   2.  1.  0 /  2.  1.  0
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  2.101 /  1.  2.101
  libpostproc    53.  3.100 / 53.  3.100
[matroska,webm @ 0x17e9c80] Read error at pos. 245 (0xf5)
[matroska,webm @ 0x17e9c80] Duplicate element
[matroska,webm @ 0x17e9c80] Read error at pos. 77 (0x4d)
[matroska,webm @ 0x17e9c80] Read error at pos. 105 (0x69)
[matroska,webm @ 0x17e9c80] Duplicate element
[matroska,webm @ 0x17e9c80] Read error at pos. 245 (0xf5)
[matroska,webm @ 0x17e9c80] Duplicate element
    Last message repeated 1 times
file.mkv: End of file

I'm not familiarized with matroska, but perhaps one could expect not to display anything when trying to play a video like this instead of getting this amount of errors, I mean, an empty media file should not have to end up with these errors, they simply should play nothing because they contain nothing. Don't they?