Hi every one! I have the same problem with the blockMesh file attached. when running,
 

/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
object blockMeshDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

convertToMeters 1;

vertices
(
(0 0 0) //0
(0.914 0 0) //1
(0 1.93 0) //2
(0.914 1.93 0) //3
(0 3.93 0) //4
(0.914 3.93 0) //5
(0 5.59 0) //6
(0.914 5.59 0) //7

(0 0 0.296) //8
(0.914 0 0.296) //9
(0 1.93 0.296) //10
(0.914 1.93 0.296) //11
(0 3.93 0.296) //12
(0.914 3.93 0.296) //13
(0 5.59 0.296) //14
(0.914 5.59 0.296) //15

(0 0 0.51) //16
(0.914 0 0.51) //17
(0 1.93 0.51) //18
(0.914 1.93 0.51) //19
(0 3.93 0.51) //20
(0.914 3.93 0.51) //21
(0 5.59 0.51) //22
(0.914 5.59 0.51) //23

(8.334 5.59 0) //24
(8.334 6.504 0) //25
(6.404 5.59 0) //26
(6.404 6.504 0) //27
(2.404 5.59 0) //28
(2.404 6.504 0) //29
(0.914 5.59 0) //30
(0.914 6.504 0) //31

(8.334 5.59 0.296) //32
(8.334 6.504 0.296) //33
(6.404 5.59 0.296) //34
(6.404 6.504 0.296) //35
(2.404 5.59 0.296) //36
(2.404 6.504 0.296) //37
(0.914 5.59 0.296) //38
(0.914 6.504 0.296) //39

(8.334 5.59 0.51) //40
(8.334 6.504 0.51) //41
(6.404 5.59 0.51) //42
(6.404 6.504 0.51) //43
(2.404 5.59 0.51) //44
(2.404 6.504 0.51) //45
(0.914 5.59 0.51) //46
(0.914 6.504 0.51) //47

(0 5.59 0) //48
(0 6.504 0) //49
(-3.546 5.59 0) //50
(-3.546 6.504 0) //51
(-7.546 5.59 0) //52
(-7.546 6.504 0) //53
(-15.546 5.59 0) //54
(-15.546 6.504 0) //55

(0 5.59 0.296) //56
(0 6.504 0.296) //57
(-3.546 5.59 0.296) //58
(-3.546 6.504 0.296) //59
(-7.546 5.59 0.296) //60
(-7.546 6.504 0.296) //61
(-15.546 5.59 0.296) //62
(-15.546 6.504 0.296) //63

(0 5.59 0.51) //64
(0 6.504 0.51) //65
(-3.546 5.59 0.51) //66
(-3.546 6.504 0.51) //67
(-7.546 5.59 0.51) //68
(-7.546 6.504 0.51) //69
(-15.546 5.59 0.51) //70
(-15.546 6.504 0.51) //71
);

blocks
(
hex (0 1 3 2 8 9 11 10) (10 10 10) simpleGrading (1 1 1)
hex (8 9 11 10 16 17 19 18) (10 10 10) simpleGrading (1 1 1)
hex (2 3 5 4 10 11 13 12) (10 10 10) simpleGrading (1 1 1)
hex (10 11 13 12 18 19 21 20) (10 10 10) simpleGrading (1 1 1)
hex (4 5 7 6 12 13 15 14) (10 10 10) simpleGrading (1 1 1)
hex (12 13 15 14 20 21 23 22) (10 10 10) simpleGrading (1 1 1)

hex (24 25 27 26 32 33 35 34) (10 10 10) simpleGrading (1 1 1)
hex (32 33 35 34 40 41 43 42) (10 10 10) simpleGrading (1 1 1)
hex (26 27 29 28 34 35 37 36) (10 10 10) simpleGrading (1 1 1)
hex (34 35 37 36 42 43 45 44) (10 10 10) simpleGrading (1 1 1)
hex (28 29 31 30 36 37 39 38) (10 10 10) simpleGrading (1 1 1)
hex (36 37 39 38 44 45 47 46) (10 10 10) simpleGrading (1 1 1)

hex (30 31 49 48 38 39 57 56) (10 10 10) simpleGrading (1 1 1)
hex (38 39 57 56 46 47 65 64) (10 10 10) simpleGrading (1 1 1)
hex (48 49 51 50 56 57 59 58) (10 10 10) simpleGrading (1 1 1)
hex (56 57 59 58 64 65 67 66) (10 10 10) simpleGrading (1 1 1)
hex (50 51 53 52 58 59 61 60) (10 10 10) simpleGrading (1 1 1)
hex (58 59 61 60 66 67 69 68) (10 10 10) simpleGrading (1 1 1)
hex (52 53 55 54 60 61 63 62) (10 10 10) simpleGrading (1 1 1)
hex (60 61 63 62 68 69 71 70) (10 10 10) simpleGrading (1 1 1)
);

edges
(
);

boundary
(
inletMain
{
type patch;
faces
(
(24 25 33 32)
(32 33 41 40)
);
}

inletBranch
{
type patch;
faces
(
(0 1 9 8)
(8 9 17 16)
);
}

lowerWall
{
type wall;
faces
(
(0 1 3 2)
(2 3 5 4)
(4 5 7 6)
(24 25 27 26)
(26 27 29 28)
(28 29 31 30)
(30 31 49 48)
(48 49 51 50)
(50 51 53 52)
(52 53 55 54)
);
}

middleLayer
{
type patch;
faces
(
(8 9 11 10)
(10 11 13 12)
(12 13 15 14)
(32 33 35 34)
(34 35 37 36)
(36 37 39 38)
(38 39 57 56)
(56 57 59 58)
(58 59 61 60)
(60 61 63 62)
);
}

atmosphere
{
type patch;
faces
(
(16 17 19 18)
(18 19 21 20)
(20 21 23 22)
(40 41 43 42)
(42 43 45 44)
(44 45 47 46)
(46 47 65 64)
(64 65 67 66)
(66 67 69 68)
(68 69 71 70)
);
}

fixedWallRight
{
type wall;
faces
(
(1 3 11 9)
(9 11 19 17)
(3 5 13 11)
(11 13 21 19)
(5 7 15 13)
(13 15 23 21)
(25 27 35 33)
(33 35 43 41)
(27 29 37 35)
(35 37 45 43)
(29 31 39 37)
(37 39 47 45)
(31 49 57 39)
(39 57 65 47)
(49 51 59 57)
(57 59 67 65)
(51 53 61 59)
(59 61 69 67)
(53 55 63 61)
(61 63 71 69)
);
}

fixedWallLeft
{
type wall;
faces
(
(0 8 10 2)
(8 16 18 10)
(2 10 12 4)
(10 18 20 12)
(4 12 14 6)
(12 20 22 14)
(24 32 34 26)
(32 40 42 34)
(26 34 36 28)
(34 42 44 36)
(28 36 38 30)
(36 44 46 38)
(30 38 56 48)
(38 46 64 56)
(48 56 58 50)
(56 64 66 58)
(50 58 60 52)
(58 66 68 60)
(52 60 62 54)
(60 68 70 62)
);
}

outlet
{
type patch;
faces
(
(55 54 62 63)
(63 62 70 71)
);
}
);
// ************************************************** *********************** //



--> FOAM FATAL ERROR:
Trying to specify a boundary face 4(8 9 11 10) on the face on cell 0 which is either an internal face or already belongs to some other patch. This is face 0 of patch 3 named middleLayer.

From function void Foam::polyMesh::setTopology(const cellShapeList&, const faceListList&, const wordList&, Foam::labelList&, Foam::labelList&, Foam::label&, Foam::label&, Foam::cellList&)
in file meshes/polyMesh/polyMeshFromShapeMesh.C at line 324.

topoSet::createPatchDict
 

Hallo foamers,

I know this is a old thread, but i got stuck in a similar problem. I extracted a faceSet (6 faces) using topoSet, and when i try to create patch from it, it throws following error. Please have a look at the picture, and let me know, what's wrong.
https://www.dropbox.com/sh/sxq5vj3lm...B4M8VaK2a?dl=0