I had similar issue with CF cards, where LR5 would refuse to read about 10% of the CR2 files after downloading via USB3. Download was also pretty slow and would sometimes hang for a minute or so.
What confused me was that DPP could read the files without complaint, so at first I assumed there was a bug in LR.
Since I've written a CR2 decoder myself, I tried parsing one of the bad CR2 and indeed it was corrupt. The raw data section was a few Kb too short, so the last few lines of the image were missing. So, LR was right.
I then tried with an old USB2 CF card reader and that worked fine. So I concluded it must be the USB3 interface that was causing it. Either the cable, the USB3 interface on my PC, or the camera's USB3 interface was bad.
Long story short, I have an ASUS mobo with Intel chipset which has USB3 ports, and in addition there's an ASMedia USB3 controller on board for extra USB3 ports. I had been using the ASMedia controller without thinking about it, so I switched to Intel and then everythings worked. No corrupt files, no hangs.
I'm a little worried that DPP just accepts corrupt CR2 files without any warning. I wonder how many users have big CR2 libraries with many partially corrupt files without even knowing about it.