There are two possibilities here depending on whether or not the data for the entity was deleted when it was removed.
If data is not deleted then the entity will display until the data is purged based on your current purge settings (from Configuration > Data purging). By default the longest this should be is 2 months and then it should be cleaned up.
If you have ticked the option to delete the data when you remove the entity it will take the UI a small amount of time to remove the associated data and then the entities themselves - please allow up to 5-10 minutes for the UI to catch up with the process, especially if you have a large data repository.
There was an issue fixed in 12.0.12 where if you have a SQL instance on a node of a cluster and remove that cluster node from the cluster (in Windows), the card for the SQL instance remains. If you are seeing this issue, please please update to a version 12.0.12+.