1. You cannot distribute an interpreter that can be used for running program code downloaded from the internet. So, for example, your user can save their script and use it themselves but they cannot give it to others (except perhaps through the app store bundled as an app itself).
2. Your interpreter cannot dynamically generate binary code so JIT compilers that generate binary code on-the-fly are not allowed.
edit: For example, LuaJIT cannot do JIT compilation on iOS but it can do JIT compilation for higher performance on Android.
However, I speculate even the 2nd restriction is partly for business reasons because it prevents some third-party toolkits (such as those compiling to LLVM) from achieving high performance. You might remember that Adobe was compiling Flash to LLVM to allow devs to port their Flash apps to iOS, but since LLVM cannot do proper JIT compilation on iOS, it will reduce performance.
FWIW: WinRT imposes both the restrictions above. Android technically doesn't impose either for sideloaded apps. But if you want to distribute app through Google Play, the 1st restriction is indeed imposed.
I hadn't considered this before, but that means that you could potentially use JS as an intermediate representation for other languages in order to leverage Safari's JIT under iOS. Probably too inefficient to be worthwhile for any language that isn't a dialect of JS, but an intriguing concept nonetheless.
Javascript in Safari is jitted - but JS in a UIWebView used by a third-party app is not.