How to reproduce:

1. Open attached project
2. Open the scene Scenes/Main.unity
3. Play the scene
- Note the cube appears red, even though it should have a different texture
- By opening the script Scripts/AssignTextureAtRuntime.cs and commenting out Line 28, the issue is fixed (the cube gains a texture)

- Reproduced in Version 5.4.0b15 (2e995a1aa11c), Version 5.3.4f1 (fdbb5133b820), Version 5.3.4p3 (b902ad490cea), Version 5.0.4f1 (1d75c08f1c9c)

- By Design: The behaviour, where the reference to a material that is assined via the array isn't the same as the one one gets out when querying it again, has been in place since at least 5.0 (based on the code and behaviour) and is expected to be as such.