If you specify --precompilejsps=false (the default setting) when you deploy an application, this problem does not occur. Be aware that the first use of the application triggers the JSP compilation, so the response time to the first request is longer than for later requests.
Note also that if you do precompile, you should stop and restart the server before undeploying or redeploying the application. The shutdown frees the locked JAR files so the undeployment or redeployment after the restart can succeed.