Aren't prone and Y raises supposed to work the lower trapezius? whenever I do them my upper and middle traps get an absurd pump, it feels like they are going to explode but nothing happens to the lower trap.
A lot of times it's because you're handling more weight than your lower traps can handle (i'm assuming you're doing this with weights or a band) or because you haven't learned to engage them properly with the right cues. So your upper traps come into play to help compensate. Try other exercises as well and get a feel for the lower traps firing. Developing those cues and going lighter (without weights if you have to). I personally found middle trap raises and partial dip shrugs on the assisted pull up machine really helpful in targeting my lower traps.