It may be possible the application may have created a thread that was left running in the background and tomcat was unable to successfully stop it ( it sometimes happens ) . But I cannot be sure since I am not aware of your web application. Look at the logs when you stop the application to see whether the application has stopped completely or is there any thread still left that is being executed on tomcat .
Muhammad Saif Asif Mirza
OCJA(5/6) OCJP(6) OCJWCD(6)
subject: the action can't be completed because the file is open in apache tomcat 6.0