Update: I realised I didn't have the background transparent in one of my layers but then encountered the real problem.
With the scene I'm creating that involves space, I've done some stars and planets however this is where the problem lies.
The stars are appearing over the planets like a top layer would. I've only just started using nodes recently but before this I could go into the render layers section in the default window and disable sky which would give me a transparent background but now with the nodes enables it seems I can't find this option anymore.
Does anyone know how to do this with nodes? Screenshots would be incredibly helpful as well :)
Also due to copyright I can't upload the model or any part of the file, sorry guys :(