This links:
platform :ios, '8.0'
pod 'Ambly', :git => 'https://github.com/mfikes/ambly', :branch => 'jsc-c-api'
pod 'Ejecta', :git => 'https://github.com/swannodette/Ejecta', :branch => 'podspec'
Below uses my fork of your Ejecta, and also links. I mucked with getting rid of the JavaScriptCore framework and renaming the static lib so it can be included. (This works, but it is not clear if needed over just using your fork).
platform :ios, '8.0'
pod 'Ambly', :git => 'https://github.com/mfikes/ambly', :branch => 'jsc-c-api'
pod 'Ejecta', :git => 'https://github.com/mfikes/Ejecta', :branch => 'podspec'
Both of the above produce the warning and so does your fork of Ejecta, if you run it by itself (perhaps the warning is benign; if you search for Class JSWTFMainThreadCaller is implemented in both you will see being mentioned in passing in several Ejecta tickets):
objc[15803]: Class JSWTFMainThreadCaller is implemented in both /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/System/Library/Frameworks/JavaScriptCore.framework/JavaScriptCore and /Users/mfikes/Library/Developer/CoreSimulator/Devices/A4003DFC-2036-4831-AAF6-5A351196BEB2/data/Containers/Bundle/Application/0A294585-E24E-45E4-A7E1-B316DDAFAAB9/Ejecta.app/Ejecta. One of the two will be used. Which one is undefined.
2015-05-20 17:39:33.811 Ejecta[15803:217685] Creating ScreenCanvas (2D): size: 375x667, style: 375x667, retina: yes = 750x1334, msaa: no