FNAC Port displayed 6 , Total 12

Are there any configuration differences in the switch between the ports that are appearing and those that are not? You can try a ‘Resync Interface’ to see if they appear, otherwise, the integration with this switch needs to be checked.

Additionally to Emirjon suggestion,

Did you add the device by SNMP only or by SSH as well?

When you click on “Validate Credentials” did both SNMP and SSH succeeded?

You can use the below steps to see if FNAC has any issue when communicating with the device, like wrong command or wrong output.

1. Enable the debug:
   device -ip <device-IP> -setAttr -name DEBUG -value "TelnetServer ForwardingInterface"

2. Then run:
   tail -f /bsc/campusMgr/master_loader/logs/output.master

3. Then run some operations on the device, e.g.:
   → Click validate credentials for the device
   → Click L2/L3 poll
   → Resync interface

You may also have a look at the SNMP output to see if all interfaces are correctly listed, because I remember sometimes I’ve found some devices with SNMP issue, like output truncated ...etc.

Hope it helps.

Additionally, you can enable the debug for the Device integrated on Fortinac GUI:

Perform validate credentials for the device, run L2 poll and Resync interface.
Ensure that you are using the admin privileges on this integration.

Article:

 Collect the grabsnapshot log and open a ticket with FortiNAC support Team.

Thanks