Hello everyone,
I am currently working on a project, and I came by this problem in the compositor. I rendered all my objects on different layers, but when I added them together the spaceship appears very transparent, I looked where I could, but I still cant find the source of the problem. I wanted to know if any of you would know the issue.
Here is the blend file: http://www.pasteall.org/blend/42561
Many thanks in advance 
When you add elements, they add. Add operation is not masked by alpha channel and you don’t have alpha channel enabled in renders anyway. Check the Transparent checkbox in Film panel under Render settings and use Alpha Over node if you have to composite foreground elements that are not additive light elements. Alpha Over for all planets, spaceships, meteors and whatnot. Add for glows, streaks, light passes etc.
Thank you very much!