Since I'm not the only one this is happening to, I just want to give a heads up to those going after the trophies; it seems like the later ones are buggy/glitched(could possibly be earlier ones too?) whereas fulfilling the requirements doesn't unlock the trophies.
The trophies I've had this issue with so far are Lv60, Clear Kelsaik's Nest, Clear Labyrinth of Terror. I've even done Kelsaik's Nest multiple times with no unlock still. I'm pretty sure I killed all the WBs for Shara Boss as well, but its possible I might have forgot one and that's why that particular one didn't unlock for me.
Some others are reporting not getting the level 65 trophy either despite being 65, along with some others as well. Hopefully this gets fixed soon and you don't have to redo the requirements to unlock them