Are you per chance confusing the names here? because the silent temple and the abandoned temple are two VERY different dungeons. And yes, all the crystals damia tells you about can be completed so you've deffinitely missed something in the forest. And the bees are completely unrelated to the main quest by the way.
As for teh kitsune. She is at the campsite next to the royal city where you took the wagon to sneak in during the main story but only after you've done the Royal city part of the main story.