I don't have access to the log files of the specific problem, since i don't work anymore for the company, where we had the problem, but i pinged my former colleague, to reproduce the problem.
The situation was the following: 
A test class, which had some fields annotated with @Inject, where a Stateless bean should be injected. However, the annotations on the bean were wrong, so WebSphere threw an exception because of unsatisfied dependencies. The application was deployed, but couldn't be started, and also Arquillian didn't undeploy at the end of the test. If we then reexecuted the test, the application already existed in WebSphere, and deployment failed in Arquillian.

I hope, i can deliver a sample application next week, so that we can reproduce that problem.