Not all MKV files are wrongly detected after upgrading file and
libmagic1 to version 5.04. Only files produced by the new mkvmerge from
mkvtoolnix-4.0.0-0ubuntu3. Matroska files produced by the previous
mkvmerge are detected alright:

Mime Type                         Muxing application
application/octet-stream libebml v1.0.0 + libmatroska v1.0.0
video/x-matroska              libebml v0.7.7 + libmatroska v0.8.1 

An inspection of  the mis-identified files shows that they have a little
more info at the beginning:

$ hexdump -C new-matroska-file.mkv | head -7
00000000  1a 45 df a3 a3 42 86 81  01 42 f7 81 01 42 f2 81  |.E...B...B...B..|
00000010  04 42 f3 81 08 42 82 88  6d 61 74 72 6f 73 6b 61  |.B...B..matroska|
00000020  42 87 81 02 42 85 81 02  18 53 80 67 01 00 00 00  |B...B....S.g....|
00000030  76 a4 26 1f 11 4d 9b 74  be 4d bb 8c 53 ab 84 15  |v.&..M.t.M..S...|
00000040  49 a9 66 53 ac 82 10 03  4d bb 8c 53 ab 84 16 54  |I.fS....M..S...T|
00000050  ae 6b 53 ac 82 10 b7 4d  bb 8e 53 ab 84 1c 53 bb  |.kS....M..S...S.|
00000060  6b 53 ac 84 76 a3 bb 1e  4d bb 8c 53 ab 84 10 43  |kS..v...M..S...C|

While the old ones are like this:

$hexdump -C old-matroska-file.mkv | head -7
00000000  1a 45 df a3 93 42 82 88  6d 61 74 72 6f 73 6b 61  |.E...B..matroska|
00000010  42 87 81 02 42 85 81 02  18 53 80 67 01 00 00 00  |B...B....S.g....|
00000020  3e 45 2b 2a 11 4d 9b 74  c0 4d bb 8c 53 ab 84 15  |>E+*.M.t.M..S...|
00000030  49 a9 66 53 ac 82 10 03  4d bb 8c 53 ab 84 16 54  |I.fS....M..S...T|
00000040  ae 6b 53 ac 82 10 b0 4d  bb 8e 53 ab 84 11 4d 9b  |.kS....M..S...M.|
00000050  74 53 ac 84 3e 44 36 01  4d bb 8e 53 ab 84 1c 53  |tS..>D6.M..S...S|
00000060  bb 6b 53 ac 84 3e 43 cd  9b ec 4f bb 00 00 00 00  |.kS..>C...O.....|

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https://bugs.launchpad.net/bugs/420963

Title:
  file command reports incorrect mime type for mkv files

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