You beat me to it. Yes, compared to what people are used to, the face is 'flipped' in photos, which is why the selfie camera on your phone also flips the image to behave like a mirror. Most photos are from far enough away that it minimises the uncanniness of the flip, but ID photos are up close. Another thing that can be offputting is that the image is static, when people are used to seeing their faces moving. The harsh lighting for ID photos can also highlight features that people aren't used to focusing on.