Steps to reproduce:

1. Open attached project
2. Project has two scenes: "BugScene" and "NormalScene". Difference is that sprites in "BugScene" use Rigidbody2D while sprites in "NormalScene" do not
3. Open "BugScene"
4. In hierarchy, expand "RootObject" and select "Child02"
5. In inspector, notice that it has Rigidbody2D. Also, transform X = Y = 2
6. Run scene and in game view click "Set Scale" button
7. Notice that sprite is scaled and moved to X = Y = 6. Also, if sprite is selected notice that BoxCollider2D and actual sprite locations differ

Workaround: Use Vector3 with Z = 1

Not reproducible: 5.3.4f1
Reproduced with:
5.4.0b1 (if sprite is moved in scene view then BoxCollider2D and sprite location becomes the same),
5.4.0b10 (BoxCollider2D and sprite location is same only when transform X = Y = 0)