I had a similar issue but on unifi gateway lite after upgrading to 1gig fibre, I couldn't get above about 250-300mbps, even wired. Everything looked good in the unifi app. Turns out in the unifi web UI there was a "use hardware acceleration" checkbox for the gateway that was unticked and not even visible in the app. Ticked that and now I am getting 900+mbps
I also sometimes have alerts saying more than one device is using the same IP address (DHCP issues) but it won't tell me which ones! At least give me the MAC addresses!
Unifi's stuff is great, but the software is sometimes infuriating.
Other trap is some of the unifi features, IIRC their IDS is one of them, will cut throughput if you are running it.