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I've found the misstake. This code is not doing the right matrix multiplication.

      Mat E = new Mat();
      Core.multiply(cameraMatrix.t(),fundamental, E); 
      Core.multiply(E, cameraMatrix, E);

I changed this to

      Core.gemm(cameraMatrix.t(), fundamental, 1, cameraMatrix, 1, E);

which is now doing the right matrix multiplication. As far as I can get ir from the documentation, Core.multiply is doing the multiplication for each element. not the dot product of row*col.