Discovery dns_domain and FQDN are not the same.
How discovery sets the dns_domain field:
The dns_name and dns_domain fields in a CI are usually collected in the Shazzam phase of discovery. The values returned are passed to the identification phase of the discovery. The identification phase populates/updates the field once the identification payload is processed. These are normally the dns values returned when doing an nslookup of the ip being discovered.
How discovery sets the fqdn field:
The FQDN field will depend on the device type/probe&sensor/pattern.
As an example, for windows OS devices, the following WMI fields are used:
There are properties under "Discovery Definition > Properties" which can change how the FQDN field is populated.
For more information on the properties mentioned above please review this document: Discovery properties.
As seen above, the FQDN and DNS fields of a CI are determined differently.
It is not an issue in itself that the FQDN and DNS fields of a CI do not match. The DNS values are often populated based on the results returned by the DNS server the MID server can reach, while FQDN is usually populated based on the results of scripts/queries directly against the device.
If the FQDN and dns fields must match on the environment, the following can be done to accomplish it.
If using probes, use the following properties to control how the FQDN is populated for a CI and achieve the desired behavior, may need to update probes/sensors:
If using patterns, update the pattern so that the FQDN name is set to the same as that collected via DNS.