There are some common issues faced when users create WSO2 API manager clusters. Here are some points you could follow when troubleshooting.
1. Make sure all relevant nodes are added in each others' axis2.xml cluster members. For example, if you have 4 Gateway nodes (2 Managers and 2 Workers) you need to make sure that you add all other members under cluster members (axis2.xml) , so that all the nodes are synced up. If this is not done properly, you might come across issues where some of your nodes are not updated with all changes.(Missing apis,missing edits done for apis)
You can check if all nodes are getting synced properly , by checking repository/deployment/server/synapsconfig/default/apis sections of each node and see if all published APIs are listed.
2. When you are fronting gateway nodes with a load balancer, your publisher/store node's api-manager.xml should point to the load balancer url.
3. When you are installing an external key manager (WSO2 Identity Server) , make sure that you set the url of IS, in <APIKeyManager> section of api-manager.xml.