So looking at some of these Expansion Slot Utility screencaps, I decided to re-check mine, and was shocked to see the previously 100% on A & B was now showing 125% on B... then I realised something for which I hadn't quite comprehended the full consequences - plugging in cables which change the port format (eg USB Type-C to Type-A, B, Lightning etc.) eats lane allocation (according to the utility).
It even eats 4 extra lanes when you plug in a cable that isn't connected to anything, or when you plug it into the TB ports on an MPX GPU.
Plugging in a Type-C to Type-C cable has no such effect.
I would guess
@cobra521 has a Type-C to (something else) peripheral plugged into one of their ports.
Weirdness.