The in-loop Y-Arm error signal looks equal to the beat note noise divided by the Y-Arm OL gain in the broadband-noise region (>20 Hz), which would be the case if the loop was dominated by sensor noise here.

I would re-check the Y-Arm dark noise, or at least check for coherence between the Y-Arm error signal and the beat signal above 20 Hz. The input-referred PDH box noise should not be flat there according to the LISO model, but that might be worth checking, too.