$ ffmpeg -i input.h264 -i input.flac -c copy -map 0:0 -map 1:0 /media/alex/Dane/inputs_muxed.mkv
ffmpeg version N-78936-g247fe3e Copyright (c) 2000-2016 the FFmpeg developers
  built with gcc 5.2.1 (Ubuntu 5.2.1-22ubuntu2) 20151010
  configuration: 
  libavutil      55. 19.100 / 55. 19.100
  libavcodec     57. 27.101 / 57. 27.101
  libavformat    57. 28.100 / 57. 28.100
  libavdevice    57.  0.101 / 57.  0.101
  libavfilter     6. 39.100 /  6. 39.100
  libswscale      4.  0.100 /  4.  0.100
  libswresample   2.  0.101 /  2.  0.101
[h264 @ 0x2049500] Format h264 detected only with low score of 1, misdetection possible!
[h264 @ 0x204a700] non-existing PPS 0 referenced
[h264 @ 0x204a700] A non-intra slice in an IDR NAL unit.
[h264 @ 0x204a700] decode_slice_header error
[h264 @ 0x204a700] no frame!
[h264 @ 0x2049500] Stream #0: not enough frames to estimate rate; consider increasing probesize
[h264 @ 0x2049500] decoding for stream 0 failed
[h264 @ 0x2049500] Could not find codec parameters for stream 0 (Video: h264, none): unspecified size
Consider increasing the value for the 'analyzeduration' and 'probesize' options
input.h264: could not find codec parameters
Input #0, h264, from 'input.h264':
  Duration: N/A, bitrate: N/A
    Stream #0:0: Video: h264, none, 25 tbr, 1200k tbn, 50 tbc
Input #1, flac, from 'input.flac':
  Metadata:
    ENCODER         : Lavf57.28.100
  Duration: N/A, start: 0.000000, bitrate: N/A
    Stream #1:0: Audio: flac, 48000 Hz, stereo, s16
[matroska @ 0x20699e0] dimensions not set
Output #0, matroska, to '/media/alex/Dane/inputs_muxed.mkv':
    Stream #0:0: Video: h264, none, q=2-31, 25 tbr, 1200k tbn, 1200k tbc
    Stream #0:1: Audio: flac, 48000 Hz, stereo (16 bit)
Stream mapping:
  Stream #0:0 -> #0:0 (copy)
  Stream #1:0 -> #0:1 (copy)
Could not write header for output file #0 (incorrect codec parameters ?): Invalid argument