To reproduce:

1. Download attached project "3D Top Down Shooter.zip" and open in Unity
2. Open "Main" scene
3. Select one of the game objects in the scene(such as "Some Cube" and "Player").
4. Select the Scale Tool.
5. Start scaling in any axis using the Scale Tool while holding down the Control button and scale your selected object to 3.
Note: Observe in Inspector window that your selected axis is increasing by 0.1
6. Release all buttons and repeat Fifth step

Expected Result: Observe in Inspector window that your selected axis is still increasing by 0.1
Actual Result: Observe in Inspector window that your selected axis is now increasing by 0.3...

Notes:
- This issue appears on Windows and OSX
- User said that when he is scaling, it adds double the original amount

Reproduced on Unity 5.6.4p1, 2017.1.2p2, 2017.2.0f3, 2017.3.0b6 and 2018.1.0a1