I expect the bolt head is bending relative to the threads due to the flexibility of the structure you have hidden. Bending stresses will add to the tensile stresses that you expect to see from the bolt pretension.
Plot the directional deformation on just the flat bolt head using the Coordinate axis along the bolt axis to get an estimate of the tilting of the head relative to ground. Do the same for the flat face at the thread end of the shank to see how much that face is tilting relative to ground. The difference between those two plots is the bending of the head relative to the threads.
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