MacBook Pro not booting off OS X Mavericks USB Drive
You can't use the Mac App Store build of 10.9.1 on Late 2013 Retina MacBook Pro's. That's why there is a separate 10.9.1 update for only those machines. You need to use Internet Recovery (Command-Option-R on boot) to install 10.9.1 and not the App Store version. The build number is 13B3109 for the Late 2013 rMBP while it's 13B43 for the App Store version. You can make a USB flash drive of the correct build but you need need to boot with Internet Recovery, start the install on a partition and when it restarts to finish the install you hold the option key down and boot from another partition with an already installed correct build (13B3109) and in a hidden directory on the partition you chose to install, there is an InstallESD.dmg you can then copy and use to create a USB flash installer for that build.

Now that 10.9.2 is released, the Mac App Store build will work on the Late 2013 rMBP as well as all the other Macs with the possible exception of the new Mac Pro.