Array values not being assigned to the right places

Question

I've been trying to get this code to work and i have checked it multiple times with a rubiks cube and checked if any of the values are mentioned twice, and the output deletes some values and and replaces them with already existing values.

Cube = [["W1","W2","W3"],#White 0,0| 0,1| 0,2
        ["W4","W5","W6"],#White 1,0| 1,1| 1,2
        ["W7","W8","W9"],#White 2,0| 2,1| 2,2
        ["R1","R2","R3","B1","B2","B3","O1","O2","O3","G1","G2","G3"],#Red 3,0| 3,1| 3,2 #Blue 3,3| 3,4| 3,5 #Orange 3,6| 3,7| 3,8 #Green 3,9| 3,10| 3,11
        ["R4","R5","R6","B4","B5","B6","O4","O5","O6","G4","G5","G6"],#Red 4,0| 4,1| 4,2 #Blue 4,3| 4,4| 4,5 #Orange 4,6| 4,7| 4,8 #Green 4,9| 4,10| 4,11
        ["R7","R8","R9","B7","B8","B9","O7","O8","O9","G7","G8","G9"],#Red 5,0| 5,1| 5,2 #Blue 5,3| 5,4| 5,5 #Orange 5,6| 5,7| 5,8 #Green 5,9| 5,10| 5,11
        ["Y1","Y2","Y3"],#Yellow 6,0| 6,1| 6,2
        ["Y4","Y5","Y6"],#Yellow 7,0| 7,1| 7,2
        ["Y7","Y8","Y9"]] #Yellow 8,0| 8,1| 8,2
SolvedCube = Cube
SampleCube = Cube

#White Center
Cube[0][2] = SampleCube[3][2]
Cube[1][2] = SampleCube[4][2]
Cube[2][2] = SampleCube[5][2]
#Red Center
Cube[3][2] = SampleCube[6][2]
Cube[4][2] = SampleCube[7][2]
Cube[5][2] = SampleCube[8][2]
#Blue Center
Cube[3][3] = SampleCube[5][3]
Cube[3][4] = SampleCube[4][3]
Cube[3][5] = SampleCube[3][3]
Cube[4][3] = SampleCube[5][4]
Cube[4][5] = SampleCube[3][4] 
Cube[5][3] = SampleCube[5][5]
Cube[5][4] = SampleCube[4][5]
Cube[5][5] = SampleCube[3][5]
#Orange Center
Cube[3][6] = SampleCube[2][2]
Cube[3][7] = SampleCube[1][2]
Cube[3][8] = SampleCube[0][2]
#Yellow Center
Cube[6][2] = SampleCube[5][6]
Cube[7][2] = SampleCube[4][6]
Cube[8][2] = SampleCube[3][6]
      
SampleCube = Cube

>>> print(Cube)
[['W1', 'W2', 'R3'], ['W4', 'W5', 'R6'], ['W7', 'W8', 'R9'], ['R1', 'R2', 'Y3', 'B7', 'B4', 'B7', 'R9', 'R6', 'R3', 'G1', 'G2', 'G3'], ['R4', 'R5', 'Y6', 'B8', 'B5', 'B4', 'O4', 'O5', 'O6', 'G4', 'G5', 'G6'], ['R7', 'R8', 'Y9', 'B9', 'B4', 'B7', 'O7', 'O8', 'O9', 'G7', 'G8', 'G9'], ['Y1', 'Y2', 'O7'], ['Y4', 'Y5', 'O4'], ['Y7', 'Y8', 'R9']]

this is the output with repeat values such as R3 where it should be mentioned once