I also have a problem with the USB port on the right side of my Retina MBP. The USB3.0 port on the left side works fine, even with high speed external SSD enclosures, like the OWC Mercury Extreme Pro 6G which enables me to copy large files at a sustained rate of 160-170MB/sec. Wow USB3.0 and the Mercury SSD is a FAAAAST combination connected to the Retina MBP.
However, like the forum entries about the USB3.0 ports in general on the new Retina MBP, the USB3.0 port on the RIGHT side is plagued with dropping intermittently, disconnecting my external hard drives while copying large files AS WELL AS disconnecting while just sitting there connected to an external hard drive and doing nothing.
Therefore, since I don't feel like returning my Retina MBP and waiting weeks for a replacement, I have chosen to only use the left side USB3.0 port for now.
I have my suspicions about why the right side USB port might be more problematic than the left side one. I found this older post on the internet about how "Not all USB ports are created equal on MacBooks..." that talks about how on older models of MacBooks one of the USB ports shares a USB hub with multiple other devices like the iSight camera etc. therefore making it less tolerant of heavy traffic or something like that. (http://www.wired.com/gadgetlab/2008/05/the-macbook-all/)
Therefore, I wonder if the right side USB port is sharing a USB internal hub where-as the left side one is more 'dedicated' and therefore in my case able to handle the high speed transfers/traffic I am throwing at it with my external SSDs.
I have also read that USB3.0 in general, on non-Macs, has had trouble for years. For instance, some forum entries on Apple Support Communities and other non-Apple forums has made mention that 'they' are not surprised at the problems encountered on USB3.0 external hard drives connected to the Retina MBP because Windows laptops have had a lot of flakey problems with USB3.0 for 'years'.
Also, I have recently purchased a "Buffalo" external Thunderbolt 1TB drive from OWC and have been doing Clones onto that drive for several weeks. I use SuperDuper to clone >600GB of data on my 768GB Retina MBP several times a week. And, I have (knock on wood) not had any problems with the stability of my externally connected Thunderbolt drive.
So, in my case, I am racking it up to high-speed stresses on the USB3.0 ports at least in part...and perhaps the possibility that the LEFT side USB port on the Retina MBP is more dependable and/or a more dedicated USB port than the right side one.
This doesn't really solve your problem, but it may at least help you feel like you are not alone.