Version 1.3.19 (484) OS X 10.8.3
Working on a font when I discovered that Cmd-Z no longer worked. Tried it several times to verify.
Quit Glyphs, re-opened font, Cmd-Z was working again.
There are some rare combinations that can cause the undo for one glyph the choke. This shouldn’t happen very often. If it does, could you try to remember what you did to cause it?