I've noticed this only since updating to LR 2015.12, but not sure about timing. I'm on iMac running 10.11.6. After import, all looked normal: 2 versions of each image (i import as separate files). Only after I had reformatted the camera card did I realize that what LR had imported was 2 JPEGs instead of RAW + JPEG, but not consistently. About 10-25% of the shoot was that way. I've seen it twice now. Once, I could go to the card and pull off CR2s manually, and they were fine. In the case of the reformatted SD card, I had to run card recovery software to get all the missing CR2s back and then use capture time to find the associated extra JPEGs to delete them. The JPEGS come in with [filename]-2.jpg and are right next to [filename].jpg. In the case of the reformatted card, my client ended up choosing an image that had been "lost" in this importing process and that I recovered from the card. Now that I know to watch for "-2" in the name, I can be careful. If the cards are working (I reformat often, but not low level, fortunately) and the camera is working, then I don't see how this issue is anything but a bug in LR.