I've seen this question in a few places and have encountered it myself. I believe I this is something you're seeing with respect to the Appium.app if I'm not mistaken? It turns out that the solve for me was to clone appium from git, build it, and then, via the Developer Settings, use the appium I had just built from git. Once I had done that, my problems went away.
The appium provided with the Appium.app broke in several stages: It could not create a session, was unable to launch emulators, and finally, when setup as well as possible, had this instrumentations crash which I was unable (and unwilling) to further debug.
You might want to have a look at this tutorial:
http://appium.io/slate/en/tutorial/ios.html?ruby#native-ios-automation
Follow the basic steps to cloning and building appium and then override the appium that comes with the app and you should be back in working order.