As far as DNS goes, the only thing you can do is ensure that both the FortiGate and your client PC use the same DNS server (e.g. internal DC with DNS role). Done this way, the chances for the FQDN resolving differently should be minimised.
-Make sure the DNS settings on FortiGate and the client machine are the same so that they resolve to the same IP addresses.
- If the issue still persists after configuring the same DNS both FortiGate and client machine and if the destination FQDN resolves to a different IP very frequently, try using a wildcard FQDN object instead of the full regular FQDN.
- Below are KBs that explain how a wildcard FQDN works