When I generate application with CMD, there is a code in bootstrap.js that uses document.head property to set some meta tags. However, the head property of the document object was introduced in HTML5, so any browser that isn't fully HTML5 compliant may not support it.
On Wednesday, 11/13/13 we're slated to release Cmd 4.0.1 as well.
You can always check for the latest released version of Sencha Cmd by running the command sencha upgrade --check. Once 4.0.1 is released, you can upgrade by running sencha upgrade (or, if you want the latest beta version, sencha upgrade --beta).