We ran into a similar issue recently.
The 1st link refers to filename 2013-Lexus-GS-350-front-side-view-623x389.jpeg
The 2nd link refers to filename 2013-Lexus-GS-350-front-side-view.jpegPhoton should see those as two separate images.
Unfortunately, it doesn't seem that this is true. If you look on line 262 of class.photon.php you'll see that it's striping the size information from the image unless it looks like a custom cropped image. This means that if you upload an image named something like my-image-500x500.jpg, Photon will think this is a WP-resized image and will actually pass my-image.jpg in the URL it generates. Unfortunately, in this case that image doesn't exist. In reality, the resized images will look more like my-image-500x500-300x300.jpg.