Based on your question at Mathematica.SE I assume that you simply summed up the integer values for each pixel in the raw file, and the total was greater than what you assume to be the number of incident photons.

First, how do you know what is the actual number of incident photons and are you sure your estimate is correct?

Assuming that your photon count estimate is correct, it is still not surprising that the pixel sum is greater. You seem to be assuming that one recorded photon will not cause an increase greater than 1 in the pixel value. This is not true. The values written into the raw file may be digitally amplified, i.e. multiplied by a constant factor. For example, if I import a 14-bit D7100 raw file captured at ISO 6400 into Mathematica, I find these values:

In[96]:= data = Import["~/Desktop/DSC_2935.NEF", "RawData"];

In[97]:= MinMax[data]
Out[97]= {0, 16383}

In[98]:= Take[Union@Flatten[data], 10]
Out[98]= {0, 2, 6, 8, 10, 14, 16, 18, 20, 24}

Notice that the full 14-bit range is utilized (i.e. 0..2^14-1), but all values are multiples of 2. As I remember, ISO 12800 files have multiples of 4 (though I didn't verify it at this moment).

Finally, while I am not familiar with the details of how sensors work exactly and how the data is read out, I would not be surprised if it turned out that the quantization of light (or stored electric charge) is not perfectly reflected in the recorded data. I would expect the amplification process to introduce noise and not always record the same value for the same number of quanta.