Reproduction steps:
1. Open the attached "archive" project.
2. Go to "Edit > Project Settings > Tags and Layers".
3. Expand "Tags" in the inspector.
4. Create a new tag with a "+" sign.
5. Open the "1" scene.
6. Select the "Cube" and "Cube (1)" objects in the scene.
7. Assign the new tag.
8. Repeat step step 2 and 3.
9. Remove the old "two" tag with a "-" sign.
10. Open the "NewBehaviorScript" and change "two" to a new tag name.
11. Save everything (script, scene and project).
12. Play the scene.
- Cube is deleted on trigger.
13. Build and run the project
- Cube is not deleted on trigger.

Note:
Reimport the assets to fix the issue (Project view > RMB "Assets" > Reimport All).

Reproduced with:
5.5.0b1, 5.5.2f1, 5.6.0b10, 2017.1.0a2
iPhone 6 iOS 10.2.1