Your cursor will often change or a tooltip will flicker when hovering over a secret element.
Some fragments are hidden behind the navigation UI elements. GemCraft - Chasing Shadows
Watch for "cracks" in the UI or parchment that looks slightly different from the rest of the background. Your cursor will often change or a tooltip
Look for subtle markings or peeling paper icons at the very edges of the world map. GemCraft - Chasing Shadows