Today, Apple has released the MacBook Pro Retina EFI Update v1.3 to fix this issue.
This update is recommended for MacBook Pro (Retina, 13-inch, late 2013) models.
This update addresses an issue where the built-in keyboard and Multi-Touch trackpad may become unresponsive.
You can download the update at the link below, or grab it via Software Update in the Mac App Store.
Update: Looks like Apple also released the MacBook Pro Retina EFI Update v1.2 for the 2013 15" model. The 1.2 update fixes an issue which, in rare cases, may limit the performance of the discrete graphics processor after a system wake or boot.