Question: EMC Common Mode Noise Suppresion

Dear to all experts,

I thank you first in advance for all the help and advices given. The question that I would like to ask is regarding the combination of usage in ferrite core and Y-capacitors as noise suppression. The design comparison which I would like to ask is as attached. There are two different method of placing the Y-capacitors to filter out the common mode noise. When I took this design and scan the conducted emission, I found that there are times design A is better than design B but there are times where design B is better than design A.

May I know what is the difference in noise between both design? I know that both are made to cancel out common mode noise so why is there a difference between the two design? Thanks for all the reply and help.