Looks like we cannot reproduce this. Please provide another test case to reproduce this issue.
There can be two, depending on whether you have created a separate workspace or not. When generating an application, we check to see if the target folder is inside a workspace. If so, we only generate ".sencha/app/*". Otherwise, we generate ".sencha/workspace/*" as well into the same folder.
If there is still a problem, we should examine your ".sencha/app/build-impl.xml" file. Maybe you could paste the content of that in a CODE /CODE block.