We should not use Management Studio or any native tool of SQL Server to start/stop or restart SQL Services if the SQL Server is in a clustered environment. As MSCS (Microsoft cluster service) monitors the current state of any resource that a cluster manages, if you start/stop or restart SQL Services from anything other than cluster manager, MSCS will be unable to distinguish if this change is user initiated or not. This can be a severe problem for stopping or restarting a service because in this case MSCS will conclude a user initiated stop or restart as a “System Failure” and possibly will initiate a failover to secondary node.
To avoid this situation, always use “Cluster Management” (“Failover Cluster Management”) to start, stop or restart a “Clustered” SQL Service. Technically it will do the same action to start/stop or restart SQL Service but will not confuse MSCS.