This is a common shortcoming of most load balancers - they have no concept of web applications within a node. If a node is deemed to be active, it will route requests for any application to that node, completely ignorant of the status of that web application on the node.
This specific issue was one of the primary drivers for the development of mod_cluster. mod_cluster tracks the state of each application, rather than assuming that all applications on a server are in the same state. Thus mod_cluster will never direct a request for an application to a given node unless that target application is deployed on that node.