I am glad to find this discussion, as I am experiencing the same issue. I'm on a mid 2011 iMac, 10.11.2, and I use a Nikon D3300 DSLR camera. I first noticed the problem when in full screen mode viewing pictures full screen. The images appeared blurry, which should not be happening with my camera and my skill level.
I selected edit to try and 'fix' the image, and the blurriness disappeared: there wasn't anything wrong with the photo. I am unsure if this is happening to every photo, but I am fairly certain that it is not happening to images from my iPhone 6, and I seem to notice it more when I am viewing images full screen and using the arrow keys to move quickly between photos. As others have reported, the images are rendered correctly in the finder preview, as well as in other photo editing apps, so this seems to be an issue specifically with the Photos app.
I have a suspicion about the cause of this issue, based on a different incident with another camera, a Canon Rebel DSLR. In some cases after importing images from this camera, the Photos app subsequently 'lost' the images, which then had to be reimported. My work around was to get the images imported and then immediately quit the app. After restarting Photos, the images remain and are no longer 'lost.' I have also checked and found that the blurry issue is not apparent with images taken on the Canon camera.
I have also determined that import date does not change the issue with images taken on my Nikon: images taken and imported a year ago have the same issue as those imported two weeks ago. The issue also occurs with both jpeg and RAW format images (the RAW images seem to take longer for the Photos app to correct). Therefore, this doesn't seem to be an issue of the Photos app quietly doing background optimizing of photos over time, as 'waiting' does not fix the problem.
Based on these experiences, the suspicion that I alluded to earlier is that the Photos app is not handling images from different cameras equally, which points to compatibility issues with particular camera manufacturers, who use their own unique file systems to create and store images. Or, it might be something as simple as the image file size itself when using the Photos app on systems with less RAM and CPU power: my Nikon images are 24 megapixel, but the Canon are 18 megapixel. Does larger image size cause a delay in fully rendering the image? As noted before, my Nikon images render correctly outside the Photos app, but neither the Finder preview nor other photo editing apps have huge photo libraries to load and maintain. At this point, I could therefore ask if the Photos library size has a correlation with the problem? (probably not, as the post on using a test library suggests, but just covering the bases here)
At any rate, as Apple wants the Photos app to be the application of choice for the majority of its users, it falls to Apple to insure compatibility, especially with something as simple as jpeg or RAW images produced on a camera made by an industry leader like Nikon.
I shudder to think how many images I have deleted before noticing this issue only recently. In the 80s & 90s, we used to say of Apple, "it just works." Now, "it just works, sort of." Any other insight that those reading this discussion can offer is appreciated, and thanks to all who have contributed!
Best Regards-- Todd