Can you open developer tools using CTRL+SHIFT+I or F12 before triggering the error, and include the output from the Console?
Alternatively, is it possible for you to share a sample video that's not working?

I can not share the video, it's too big (200MB).

Output from the Console:

C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\renderer.js:81 Load C:\Users\srmp\Desktop\video.mkv
C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\ffmpeg.js:61 getFormat C:\Users\srmp\Desktop\video.mkv
C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\ffmpeg.js:69 formats matroska,webm
C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\ffmpeg.js:45 Cutting from 107.085721 to 149.593918
C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\ffmpeg.js:49 ffmpeg -i C:\Users\srmp\Desktop\video.mkv -y -vcodec copy -acodec copy -ss 107.085721 -t 42.508196999999996 -f webm C:\Users\srmp\Desktop\video.mkv-00.01.47.085-00.02.29.593..mkv
C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\ffmpeg.js:18 Error: spawn undefined ENOENT
at notFoundError (C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\node_modules\cross-spawn\lib\enoent.…:11)
at verifyENOENT (C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\node_modules\cross-spawn\lib\enoent.…:46)
at ChildProcess.cp.emit (C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar\node_modules\cross-spawn\lib\enoent.…:33)
at Process.ChildProcess._handle.onexit (internal/child_process.js:215)

Can you open CMD and run:
C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar.unpacked\ffmpeg.exe -i C:\Users\srmp\Desktop\video.mkv -y -vcodec copy -acodec copy -ss 107.085721 -t 42.508196999999996 -f webm C:\Users\srmp\Desktop\video.mkv-00.01.47.085-00.02.29.593..mkv

...And show the output?

I will add this ffmpeg output to javascript console in a later release 📝
Also I noticed that the extension has two dots "..mkv", I will fix that too in the next release.

C:\Users\srmp>C:\Users\srmp\Desktop\LosslessCut-win32-x64\resources\app.asar.unpacked\ffmpeg\ffmpeg.exe -i C:\Users\srmp\Desktop\video.mkv -y -vcodec copy -acodec copy -ss 107.085721 -t 42.508196999999996 -f webm C:\Users\srmp\Desktop\video.mkv-00.01.47.085-00.02.29.593..mkv
ffmpeg version 3.1.5 Copyright (c) 2000-2016 the FFmpeg developers
built with gcc 5.4.0 (GCC)
configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-dxva2 --enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-libebur128 --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-libschroedinger --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-lzma --enable-decklink --enable-zlib
libavutil 55. 28.100 / 55. 28.100
libavcodec 57. 48.101 / 57. 48.101
libavformat 57. 41.100 / 57. 41.100
libavdevice 57. 0.101 / 57. 0.101
libavfilter 6. 47.100 / 6. 47.100
libswscale 4. 1.100 / 4. 1.100
libswresample 2. 1.100 / 2. 1.100
libpostproc 54. 0.100 / 54. 0.100
Input #0, matroska,webm, from 'C:\Users\srmp\Desktop\video.mkv':
Metadata:
encoder : libebml v1.3.3 + libmatroska v1.4.4
creation_time : 2016-11-07 04:12:43
Duration: 00:57:18.42, start: 0.000000, bitrate: 783 kb/s
Stream #0:0: Video: h264 (High), yuv420p(tv, bt709/unknown/unknown), 720x402, SAR 1:1 DAR 120:67, 23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
Stream #0:1: Audio: aac (LC), 48000 Hz, stereo, fltp (default)
[webm @ 00000000006f7040] Using AVStream.codec to pass codec parameters to muxers is deprecated, use AVStream.codecpar instead.
Last message repeated 1 times
Output #0, webm, to 'C:\Users\srmp\Desktop\video.mkv-00.01.47.085-00.02.29.593..mkv':
Metadata:
encoder : Lavf57.41.100
Stream #0:0: Video: h264, yuv420p(tv, bt709/unknown/unknown), 720x402 [SAR 1:1 DAR 120:67], q=2-31, 23.98 fps, 23.98 tbr, 1k tbn, 1k tbc (default)
Stream #0:1: Audio: aac (LC), 48000 Hz, stereo (default)
Stream mapping:
Stream #0:0 -> #0:0 (copy)
Stream #0:1 -> #0:1 (copy)
Press [q] to stop, [?] for help
[webm @ 00000000006f7040] Only VP8 or VP9 video and Vorbis or Opus audio and WebVTT subtitles are supported for WebM.
av_interleaved_write_frame(): Invalid argument
Error writing trailer of C:\Users\srmp\Desktop\video.mkv-00.01.47.085-00.02.29.593..mkv: Invalid argumentframe= 1 fps=0.0 q=-1.0 Lsize= 0kB time=00:00:01.07 bitrate= 3.1kbits/s speed= 13x
video:35kB audio:14kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: unknown
Conversion failed!

Thanks.
I assume you are running the latest version of LosslessCut.
The format of your video has been detected as being WebM (despite the extension being mkv.)

It seems FFMPEG doesn't want to put H264 video with AAC audio into a WebM file. As far as I understand that is outside the spec of the WebM format (which only supports VP8 or VP9 video.)
Where did you get this file? As of now I can only conclude that the file is unsupported.
I guess an option would be to implement the ability to select a custom output format like matroska.

Torrent for download of sample video attached.
video.zip

I have investigated and found out that the library that I'm using to detect file type detects mistakenly detects this file as webm.
sindresorhus/file-type#67

Fixed in 2189871 and in 1.3.0