user18155: FFmpeg knows about duplicate frames in the input video stream as it outputs a message like this:

More than 1000 frames duplicated

Is there some way to tell it: "Not include duplicates into the output stream, please?"
EDIT (ADDED):
I tried this command (thanks to Mulvya):
ffmpeg -i scene.mkv -profile:v baseline -level 3.1 -vsync 0 -map 0:v  scene.mp4

and obtained the target video scene.mp4 with the same duration and (almost) identical in playback with original.
The command with full output of it is here:
>ffmpeg -i scene.mkv -profile:v baseline -level 3.1 -vsync 0 -map 0:v  scene.mp4
ffmpeg version N-83585-ga5c1c7a Copyright (c) 2000-2017 the FFmpeg developers
  built with gcc 5.4.0 (GCC)
  configuration: --enable-gpl --enable-version3 --enable-cuda --enable-cuvid --enable-d3d11va --enable-dxva2 --enable-libmfx --enable-nv
enc --enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libblur
ay --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-lib
rtmp --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-amr
wbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enabl
e-libxvid --enable-libzimg --enable-lzma --enable-zlib
  libavutil      55. 47.100 / 55. 47.100
  libavcodec     57. 80.101 / 57. 80.101
  libavformat    57. 66.102 / 57. 66.102
  libavdevice    57.  2.100 / 57.  2.100
  libavfilter     6. 73.100 /  6. 73.100
  libswscale      4.  3.101 /  4.  3.101
  libswresample   2.  4.100 /  2.  4.100
  libpostproc    54.  2.100 / 54.  2.100
Input #0, matroska,webm, from 'scene.mkv':
  Metadata:
    encoder         : libmkv 0.6.5
    TITLE           : New Project
    DIRECTOR        : Big Mac
    COMPOSER        : Big Mac
    DESCRIPTION     : This video is about New Project
  Duration: 00:03:11.93, start: 0.000000, bitrate: 1025 kb/s
    Stream #0:0(eng): Video: h264 (High), yuv420p(tv, smpte170m/smpte170m/bt709, progressive), 640x480 [SAR 1:1 DAR 4:3], 30 fps, 30 tbr
, 1k tbn, 180k tbc (default)
    Stream #0:1(eng): Audio: aac (LC), 48000 Hz, stereo, fltp (default)
    Stream #0:2(eng): Audio: ac3, 48000 Hz, stereo, fltp, 224 kb/s
[libx264 @ 00000000005c6c40] using SAR=1/1
[libx264 @ 00000000005c6c40] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
[libx264 @ 00000000005c6c40] profile Constrained Baseline, level 3.1
[libx264 @ 00000000005c6c40] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC codec - Copyleft 2003-2017 - http://www.videolan.org/x264.h
tml - options: cabac=0 ref=3 deblock=1:0:0 analyse=0x1:0x111 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 t
rellis=1 8x8dct=0 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 i
nterlaced=0 bluray_compat=0 constrained_intra=0 bframes=0 weightp=0 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40
 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'scene.mp4':
  Metadata:
    DESCRIPTION     : This video is about New Project
    TITLE           : New Project
    DIRECTOR        : Big Mac
    COMPOSER        : Big Mac
    encoder         : Lavf57.66.102
    Stream #0:0(eng): Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 640x480 [SAR 1:1 DAR 4:3], q=-1--1, 30 fps, 15360 tbn, 30
 tbc (default)
    Metadata:
      encoder         : Lavc57.80.101 libx264
    Side data:
      cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
  Stream #0:0 -> #0:0 (h264 (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 4602 fps=185 q=-1.0 Lsize=   10688kB time=00:03:11.90 bitrate= 456.3kbits/s speed= 7.7x
video:10651kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.349428%
[libx264 @ 00000000005c6c40] frame I:24    Avg QP:20.07  size: 27706
[libx264 @ 00000000005c6c40] frame P:4578  Avg QP:21.30  size:  2237
[libx264 @ 00000000005c6c40] mb I  I16..4: 20.4%  0.0% 79.6%
[libx264 @ 00000000005c6c40] mb P  I16..4:  2.0%  0.0%  2.4%  P16..4: 22.9%  4.2%  1.3%  0.0%  0.0%    skip:67.3%
[libx264 @ 00000000005c6c40] coded y,uvDC,uvAC intra: 47.9% 84.7% 30.2% inter: 4.5% 23.4% 0.6%
[libx264 @ 00000000005c6c40] i16 v,h,dc,p: 36% 26% 11% 26%
[libx264 @ 00000000005c6c40] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 31% 23% 13%  5%  7%  8%  5%  5%  3%
[libx264 @ 00000000005c6c40] i8c dc,h,v,p: 39% 26% 27%  8%
[libx264 @ 00000000005c6c40] ref P L0: 82.8% 10.5%  6.7%
[libx264 @ 00000000005c6c40] kb/s:454.58


user1871: Don't see any frames duplicated. The message you quoted - More than 1000 frames duplicated - is not ffmpeg's analysis of the input. FFmpeg duplicates or drops frames when the input and output framerates differ. You need to use the mpdecimate filter to remove duplicates in the input:
ffmpeg -i input.mp4 -vf mpdecimate,setpts=N/FRAME_RATE/TB out.mp4


18155: <p>FFmpeg knows about duplicate frames in the input video stream as it outputs a message like this:</p>

<blockquote>
  <p>More than 1000 frames duplicated</p>
</blockquote>

<p>Is there some way to tell it: "Not include duplicates into the output stream, please?"</p>

<p><strong>EDIT (ADDED):</strong></p>

<p>I tried this command (thanks to <em>Mulvya</em>):</p>

<pre><code>ffmpeg -i scene.mkv -profile:v baseline -level 3.1 -vsync 0 -map 0:v  scene.mp4
</code></pre>

<p>and obtained the target video <code>scene.mp4</code> with the same duration and (almost) identical in playback with original.</p>

<p>The command with full output of it is here:</p>

<pre><code>&gt;ffmpeg -i scene.mkv -profile:v baseline -level 3.1 -vsync 0 -map 0:v  scene.mp4
ffmpeg version N-83585-ga5c1c7a Copyright (c) 2000-2017 the FFmpeg developers
  built with gcc 5.4.0 (GCC)
  configuration: --enable-gpl --enable-version3 --enable-cuda --enable-cuvid --enable-d3d11va --enable-dxva2 --enable-libmfx --enable-nv
enc --enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libblur
ay --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-lib
rtmp --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-amr
wbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enabl
e-libxvid --enable-libzimg --enable-lzma --enable-zlib
  libavutil      55. 47.100 / 55. 47.100
  libavcodec     57. 80.101 / 57. 80.101
  libavformat    57. 66.102 / 57. 66.102
  libavdevice    57.  2.100 / 57.  2.100
  libavfilter     6. 73.100 /  6. 73.100
  libswscale      4.  3.101 /  4.  3.101
  libswresample   2.  4.100 /  2.  4.100
  libpostproc    54.  2.100 / 54.  2.100
Input #0, matroska,webm, from 'scene.mkv':
  Metadata:
    encoder         : libmkv 0.6.5
    TITLE           : New Project
    DIRECTOR        : Big Mac
    COMPOSER        : Big Mac
    DESCRIPTION     : This video is about New Project
  Duration: 00:03:11.93, start: 0.000000, bitrate: 1025 kb/s
    Stream #0:0(eng): Video: h264 (High), yuv420p(tv, smpte170m/smpte170m/bt709, progressive), 640x480 [SAR 1:1 DAR 4:3], 30 fps, 30 tbr
, 1k tbn, 180k tbc (default)
    Stream #0:1(eng): Audio: aac (LC), 48000 Hz, stereo, fltp (default)
    Stream #0:2(eng): Audio: ac3, 48000 Hz, stereo, fltp, 224 kb/s
[libx264 @ 00000000005c6c40] using SAR=1/1
[libx264 @ 00000000005c6c40] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
[libx264 @ 00000000005c6c40] profile Constrained Baseline, level 3.1
[libx264 @ 00000000005c6c40] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC codec - Copyleft 2003-2017 - http://www.videolan.org/x264.h
tml - options: cabac=0 ref=3 deblock=1:0:0 analyse=0x1:0x111 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 t
rellis=1 8x8dct=0 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 i
nterlaced=0 bluray_compat=0 constrained_intra=0 bframes=0 weightp=0 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40
 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'scene.mp4':
  Metadata:
    DESCRIPTION     : This video is about New Project
    TITLE           : New Project
    DIRECTOR        : Big Mac
    COMPOSER        : Big Mac
    encoder         : Lavf57.66.102
    Stream #0:0(eng): Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 640x480 [SAR 1:1 DAR 4:3], q=-1--1, 30 fps, 15360 tbn, 30
 tbc (default)
    Metadata:
      encoder         : Lavc57.80.101 libx264
    Side data:
      cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
  Stream #0:0 -&gt; #0:0 (h264 (native) -&gt; h264 (libx264))
Press [q] to stop, [?] for help
frame= 4602 fps=185 q=-1.0 Lsize=   10688kB time=00:03:11.90 bitrate= 456.3kbits/s speed= 7.7x
video:10651kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.349428%
[libx264 @ 00000000005c6c40] frame I:24    Avg QP:20.07  size: 27706
[libx264 @ 00000000005c6c40] frame P:4578  Avg QP:21.30  size:  2237
[libx264 @ 00000000005c6c40] mb I  I16..4: 20.4%  0.0% 79.6%
[libx264 @ 00000000005c6c40] mb P  I16..4:  2.0%  0.0%  2.4%  P16..4: 22.9%  4.2%  1.3%  0.0%  0.0%    skip:67.3%
[libx264 @ 00000000005c6c40] coded y,uvDC,uvAC intra: 47.9% 84.7% 30.2% inter: 4.5% 23.4% 0.6%
[libx264 @ 00000000005c6c40] i16 v,h,dc,p: 36% 26% 11% 26%
[libx264 @ 00000000005c6c40] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 31% 23% 13%  5%  7%  8%  5%  5%  3%
[libx264 @ 00000000005c6c40] i8c dc,h,v,p: 39% 26% 27%  8%
[libx264 @ 00000000005c6c40] ref P L0: 82.8% 10.5%  6.7%
[libx264 @ 00000000005c6c40] kb/s:454.58
</code></pre>
 1871: <p>Don't see any frames duplicated. The message you quoted - <em>More than 1000 frames duplicated</em> - is not ffmpeg's analysis of the input. FFmpeg duplicates or drops frames when the input and output framerates differ. You need to use the <a href="https://stackoverflow.com/a/37089629/5726027">mpdecimate</a> filter to remove duplicates in the input:</p>

<pre><code>ffmpeg -i input.mp4 -vf mpdecimate,setpts=N/FRAME_RATE/TB out.mp4
</code></pre>
