To reproduce:
1. Create a new project
2. Add a cube to scene
3. Drag the cube to the project window, making it a prefab
4. Open up the asset folder of the project, note the size of the prefab file
5. Save the project - note that the size increased (in my project from 5 to 9kb)

Explanation:
Unity delays the saving of changes to certain point, like "Save Scene" or "Save Project" and a few others.

Our internal version control integration does take this into account when detecting if files are modified or when you submit files, but if you are using external version control you have make sure the project is saved before you submit the files.

Just for comparison this is also true for Visual Studio. You can create a new file and disk and it will be empty. Then you can modify it in visual studio but if you try to submit the file before saving it, the submitted file will be empty. Unless you use a version control plugin in visual studio