If the SQL server has many virtual cluster of SQL DB instances, those are not collected by SQL discovery correctly.
It will show the error during discovery: "A network-related or instance-specific error occurred while establishing a connection to SQL Server"
Bug 413: SQL Discovery does not support SQL Server cluster as a target
To workaround this limitation of the product, Try using cluster node names, not main cluster name. To test this, please create a new SQL discovery for one cluster. Scope the discovery by typing in each cluster node FQDN. Run the discovery.
This will improve in future release. Enhancement request Item 774: Add support for virtual SQL clusters as discovery targets
