Error when inserting sidx atoms

[Alan]

bash-3.2$ /Volumes/storage/render/ffmpeg/ffmpeg -y -i "/Volumes/storage/render/media/in/input.mp4" -movflags global_sidx+frag_keyframe -frag_duration 1000 -codec:v libx264 -profile:v baseline -pix_fmt yuv420p -b:v 500k -codec:a aac -b:a 96k -strict -2 -s 426x240 -threads 0 "/Volumes/storage/render/media/out/output.mp4"
ffmpeg version N-76633-g4746653-tessus Copyright (c) 2000-2015 the FFmpeg developers

built with Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
configuration: --cc=/usr/bin/clang --prefix=/opt/ffmpeg --as=yasm --extra-version=tessus --enable-avisynth --enable-fontconfig --enable-gpl --enable-libass --enable-libbluray --enable-libfreetype --enable-libgsm --enable-libmodplug --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopus --enable-libschroedinger --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libvidstab --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzmq --enable-version3 --disable-ffplay --disable-indev=qtkit --disable-indev=x11grab_xcb
libavutil 55. 5.100 / 55. 5.100
libavcodec 57. 13.102 / 57. 13.102
libavformat 57. 13.100 / 57. 13.100
libavdevice 57. 0.100 / 57. 0.100
libavfilter 6. 14.101 / 6. 14.101
libswscale 4. 0.100 / 4. 0.100
libswresample 2. 0.100 / 2. 0.100
libpostproc 54. 0.100 / 54. 0.100

Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/Volumes/storage/render/media/in/input.mp4':

Metadata:

major_brand : qt
minor_version : 537199360
compatible_brands: qt
creation_time : 2015-10-27 16:59:17

Duration: 00:00:10.64, start: 0.000000, bitrate: 3098 kb/s

Stream #0:0(eng): Audio: aac (LC) (mp4a / 0x6134706D), 48000 Hz, stereo, fltp, 83 kb/s (default)
Metadata:

creation_time : 2015-10-27 16:59:41
handler_name : Apple Alias Data Handler

Stream #0:1(eng): Video: h264 (Main) (avc1 / 0x31637661), yuv420p(tv, bt709), 1280x720, 3008 kb/s, SAR 1:1 DAR 16:9, 29.97 fps, 29.97 tbr, 90k tbn, 180k tbc (default)
Metadata:

creation_time : 2015-10-27 16:59:41
handler_name : Apple Alias Data Handler
encoder : H.264

[libx264 @ 0x7fc1d3012e00] using SAR=640/639
[libx264 @ 0x7fc1d3012e00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
[libx264 @ 0x7fc1d3012e00] profile Constrained Baseline, level 2.1
[libx264 @ 0x7fc1d3012e00] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft 2003-2015 - ​http://www.videolan.org/x264.html - 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 trellis=1 8x8dct=0 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=7 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=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=abr mbtree=1 bitrate=500 ratetol=1.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Volumes/storage/render/media/out/output.mp4':

Metadata:

major_brand : qt
minor_version : 537199360
compatible_brands: qt
encoder : Lavf57.13.100
Stream #0:0(eng): Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 426x240 [SAR 640:639 DAR 16:9], q=-1--1, 500 kb/s, 29.97 fps, 30k tbn, 29.97 tbc (default)
Metadata:

creation_time : 2015-10-27 16:59:41
handler_name : Apple Alias Data Handler
encoder : Lavc57.13.102 libx264

Stream #0:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 96 kb/s (default)
Metadata:

creation_time : 2015-10-27 16:59:41
handler_name : Apple Alias Data Handler
encoder : Lavc57.13.102 aac

Stream mapping:

Stream #0:1 -> #0:0 (h264 (native) -> h264 (libx264))
Stream #0:0 -> #0:1 (aac (native) -> aac (native))

Press [q] to stop, ? for help
frame= 124 fps=0.0 q=25.0 size= 182kB time=00:00:04.88 bitrate= 305.0kbits/frame= 179 fps=179 q=27.0 size= 353kB time=00:00:06.61 bitrate= 437.2kbits/frame= 317 fps=211 q=25.0 size= 766kB time=00:00:10.64 bitrate= 589.2kbits/[mp4 @ 0x7fc1d3010400] Starting second pass: inserting sidx atoms
Non-consecutive fragments, writing incorrect sidx

Last message repeated 711 times

frame= 319 fps=202 q=-1.0 Lsize= 913kB time=00:00:10.68 bitrate= 699.5kbits/s
video:678kB audio:125kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 13.572538%
[libx264 @ 0x7fc1d3012e00] frame I:5 Avg QP:20.79 size: 11995
[libx264 @ 0x7fc1d3012e00] frame P:314 Avg QP:23.62 size: 2019
[libx264 @ 0x7fc1d3012e00] mb I I16..4: 20.0% 0.0% 80.0%
[libx264 @ 0x7fc1d3012e00] mb P I16..4: 0.9% 0.0% 2.6% P16..4: 36.6% 17.0% 6.8% 0.0% 0.0% skip:36.1%
[libx264 @ 0x7fc1d3012e00] final ratefactor: 21.26
[libx264 @ 0x7fc1d3012e00] coded y,uvDC,uvAC intra: 66.7% 84.4% 57.9% inter: 16.3% 31.1% 3.8%
[libx264 @ 0x7fc1d3012e00] i16 v,h,dc,p: 28% 26% 21% 25%
[libx264 @ 0x7fc1d3012e00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 18% 25% 15% 6% 8% 7% 9% 6% 7%
[libx264 @ 0x7fc1d3012e00] i8c dc,h,v,p: 50% 26% 15% 8%
[libx264 @ 0x7fc1d3012e00] ref P L0: 75.7% 14.4% 9.9%
[libx264 @ 0x7fc1d3012e00] kb/s:521.63
[aac @ 0x7fc1d3025a00] Qavg: 526.973
bash-3.2$

[Carl Eugen Hoyos]

Is a specific input file needed to reproduce this issue?

[Alan]

Attached "input.mp4" which will reproduce the issue.