How can a common mode choke filter differential noise?
You're wiring the common mode filter wrong (look at the dots!). In this way, you're creating a differential mode filter. The current of V1, in fact, enters  both on L2 and on L1 from the dot side. This way, the magnetic flux, instead of cancelling each other, is summed. 

In a common mode filter, instead, the differential current enters the first winding the one dot, and exits the other winding from the dot.