I confirmed the warning comes from the IC2 VREF pad6 correction ruleset, which forces VREF’s position to X = 1.25 mm, Y = 0.95 mm using !important; it does not itself indicate an electrical error.
In Agent mode, I’ll try removing only the !important flags, verify that VREF stays at the corrected position, and recheck the warning—rather than deleting the pad correction blindly.