There are three scenarios you may be encountering:
Scenario A: A single host running in EC2 might have an instance ID (i-abcd1234), a generic hostname provided by EC2 based on the host’s IP address (ip-192-0-0-1), and a meaningful host name provided by an internal DNS server or a config-managed hosts file (myhost.mydomain).
Datadog creates aliases for hostnames when there are multiple uniquely identifiable names for a single host. It takes about 10-20 minutes for the single host’s duplicate names to be aliased, this will not impact your billing. You can read more about hostnames here.
Scenario B: When installing the agent on an AWS EC2 instance, you might see duplicated hosts on the Infrastructure page or Host Map for a few hours if you manually set the hostname in the agent’s configuration. This second host will disappear a few hours later, and won’t affect your billing.
Scenario C: In some rare cases the AWS endpoint that provides the instance-id information that Datadog uses to reconcile agent-based host records with the matching AWS-based host record. Restarting the agent will cause the agent to attempt to re-sync with the instance-id endpoint. You can confirm the availability of this endpoint by running the following command from the host in question - curl http://169.254.169.254/latest/meta-data/instance-id