First of all assuming you know the start and stop duration; we will add key-frames at that duration.
#ffmpeg -i a.mp4 -force_key_frames 00:00:09,00:00:12 out.mp4

Now you can again try to cut the video from specific time.
#ffmpeg -ss 00:00:09 -i out.mp4 -t 00:00:03 -vcodec copy -acodec copy -y final.mp4