If some plants show the new 3D models while others stay flat, work through these checks.
Quick checks
1. Is the pack selected? Open Options > Resource Packs and confirm Fragrant Flowers Expanded is in the Selected column, not Available.
2. Is something overriding it? Move it to the top of the Selected list, above any other pack that changes plants, then click Done.
3. Did resources finish reloading? If the change looks only half applied, press F3 + T to reload resource packs, or restart the game.
When only certain plants stay flat
- Plants from other mods: only the listed supported plants get new looks. These are Bushier Flowers bushes, the Biomes We've Gone vanilla flower variants, the Just Dandy Fluffy
Dandelion, the Habitat Blowball, and the Adorable Hamster Pets 
sunflower. Plants from other mods will keep their original appearance. - Supported mod plants still flat: check that the supported mod is installed and loading. Also make sure any resource pack that mod provides sits below Fragrant Flowers Expanded.
- Newer vanilla plants: the pack covers plants from recent updates. If one looks unchanged, another pack higher in the list is the likely cause.
Shaders
If you use shaders through a loader such as Iris or OptiFine and the flowers look odd, switch shaders off in the video settings. If the flowers then look correct, the shader pack's handling of plants is the cause, not this resource pack.