I noticed that if you cook with -allmaps instead of specifying each map like -map=map1+map2..., that it seems to cook all assets in your game's content folder, whether or not it's used in any maps or not.
This seems to also happen if you use the "package project" option in the editor, as that must use the -allmaps flag.
Expected results: Only assets that are referenced in some map are cooked. For example, if there is only one map in your project named "test", running the cooker with -map=test and -allmaps should cook exactly the same assets and produce exactly the same results in the cooked folder.
Not specific to iOS, also happens with -targetplatform=WindowsNoEditor
Head over to the existing Questions & Answers thread and let us know what's up.