Unity3D projects should have the following file structure:
Assets /
Animations
Art /
Materials
Editor
Fonts
Models
Music
Physic Materials
Prefabs /
* More folders here for organization *
Scenes
Sounds
Scripts /
* More folders here for organization *
Shaders
Terrains
Additional folders may be in here depending on the project, such as NGUI or Standard Assets.
If you have files in the wrong folder, happy Slapsgiving.