Ya, it looks like someone screwed up with the connections. The Grounded Conductor on the Primary side [the 480Y277 side] should not have been run to the transformer to begin with, let alone being re-grounded in the transformer enclosure.
Don hit the nail on the head with the code violation, too.
What this will do is cause objectional current to flow on the conduits for the 480Y277 system. The current drawn for L-N loads will try to flow on both the conduit and in the Grounded Conductor. This happens even if the bond is no where near any L-N loads. They just need to be flowing that direction, or through that certain subpanel [or gear section], for this to happen.
Are the Conduits for subfeeders and the transformers by chance hotter than average? Do they spark when a coupling is opened ? Are you noticing any Locknuts that appear to be discolored, have a tarnished spot around the KOs where the connector enters, or even some Ash like deposits just "showing up"?
Those are classic cases I have seen where a Grounded Conductor was mistakenly re-grounded somewhere on the local system.
Give your self, plus your Inspector a pat on the back for spotting this! It can be a small problem, or a 911 problem!
Keep up with the sharp eye!