Well from what I understood, Cocoon does not support layout-by-layout loading. This means when your game starts, Cocoon will load all the sprites in memory, project-wide, regardless of which layout is being displayed. If you have a small game with two or three layouts, this should not be a big deal. If your game contains many layouts with many different assets, this is more of problem as it will load everything in the RAM, quickly reaching the phone's memory limit if you happen to use big images. Iphone "only" has 512mb of RAM, lots of which is already used by the OS and other process running in background. So if you happen to have over 200mb of images in your game loading at the same time, you're in trouble. Some people said their game won't load at all for that reason.
I have read there are problems with some sounds not playing too.
The big issue is that people of Cocoon don't seem to be in a hurry to fix those problems. Instead they prefer to add new features. Again, this is based on what I could read on this forum.