I have seen a repeated problem on my project when I upgraded from AS 4.1.2 to 4.2.1. I will make a simple change, and when I try to run (which invokes a build request) I see the error I have documented in this SO post.
I have also seen a problem whereby when I ask for a full rebuild (Build -> Rebuild Project) I get an error that AS cannot delete the 'build' directory. In fact, checking for the build directory in my file system shows that it is, in fact, gone. When I immediately request a rebuild a second time, it succeeds.
I have documented this in a bug report here.
I cannot imagine what setting might be in my project that could cause either of these errors, but hoping someone here might have an idea.
If I create a brand new sample project in the same top level directory (all my projects are in directories off of C:\BLD\AndroidStudioProjects), neither of the errors mentioned above occurs.