Reproduction steps:
1. Open the attached "archive" project.
2. Connect a device.
3. Launch the "Unity Remote 5" on a device.
4. Go to "Edit > Project Settings > Editor" and select a connected device.
5. Play the "MOOshootStormPreLoad" scene in the Editor.
6. Wait for it to load.
7. Click on a red play button.
8. When the ship spawns, click on the top left corner of the screen.
9. Click the stop (square) button twice.
10. Click play.
- Note that the old ship despawned and a new one spawned.
11. Build it for iOS device.
12. Repeat steps 6-10.
- Note that the old ship from the previous game is still there.

Reproduced with:
- 5.5.0b1
- 5.5.0b9
- iPad Air 2 9.3.2

Notes:
- May be a regression(noted by user), but project doesn't play well on older versions.
- User discovered, that "controlGraphic", "playerParent", and "levelDisplay" tags doesn't work.