A common mistake is configuring the authentication group in separate policies.
The FortiGate works by matching the source and destination IP addresses to the policy. If the addresses match, it will check which groups are allowed on that policy. If the user is allowed as part of the groups on that policy, traffic will be allowed. However, if the user is not part of the allowed groups, traffic will be dropped at that policy.ScopeFortiGate, Authentication, FSAE.Solution
In the example above, if the user is part of Group A, they will be allowed through. However, if the user is part of group B, traffic will be dropped at policy 2. No traffic will reach policy 3.
The correct way to configure two groups is to configure two sub-policies on the same identity based policy:
In this way the traffic will be allowed by both groups A and B.
Technical Note : FSAE Troubleshooting Guide