Each of the scenes of your project has its own background color. The background color of your project is only visible if a scene background is transparent, otherwise it is the background color of the scene which first loads when navigating.
To fix this, you can either change the background color of each of your scenes or use an experience background layer that will be global for all your scenes. For more details about creating a background, I invite you to read the following article: http://support.intuilab.com/kb/a-quick-overview/creating-a-background-for-your-experience
Please let me know if you need more details.