It seems that "sencha app upgrade" has some problems removing the previous touch files (and thus not copying in new ones), if hidden files have been added somewhere down the directory tree.

I noticed this after having added the touch folder subversion (thereby adding ".svn"-folders in every folder). Forcibly removing the touch directory, and re-running "sencha app upgrade" worked fine.

System info:
Upgrade was from ST 2.1 to 2.2.
Sencha Cmd v3.0.0.250
java version "1.7.0_10"
Java(TM) SE Runtime Environment (build 1.7.0_10-b18)
Java HotSpot(TM) 64-Bit Server VM (build 23.6-b04, mixed mode)
Darwin kepler-64.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64