We have an environment that consist of flat network(not our choice), When I configure a 802.3ad Agg with the onsite switch Port channel and vlan interface in vlan1(not our choice) on the FW. I cannot get traffic to flow unless I change the native vlan to something else and trunk it up from the switch. I believe the Fortigate is expecting tagged vlan traffic (vlan 1 in this case) and drops the traffic. As you have to specify the vlan tag when creating the SVI on the FW.
The Fortinet Security Fabric brings together the concepts of convergence and consolidation to provide comprehensive cybersecurity protection for all users, devices, and applications and across all network edges.