Currently I'm just confused about this, but here goes.
During development, I see no problem while running directly from Xcode to an attached device. Also when making Appstore builds directly in Xcode, and installing these builds onto device, I see no problem.
Only when I use my Jenkins setup which exports from SVN, uses Shenzen's ipa tool to build and then "deliver" to deliver to iTC TestFlight, I see consistent incorrect output on device (tested on several iPhone 5/5s, 6 plus) after downloading from TestFlight. Here are actual screenshots of the "Settings" part of the app. Notice how the spriteframes of buttons are offset in the "automated" build. Note that the graphics are all in the same spritesheet generated with SpriteBuilder.
As all seems normal as long as I build and install through Xcode, I'm not sure I can label this an issue with cocos2d itself, but it's worth a shot
The general error seems to be that the spriteframes are rendered with an offset a few pixels/points too high, so it looks like the actual buttons appear lower, and also whatever is in the spritesheet at that position also appear as "garbage" in the upper part of the button. In the case of the white button here, the close button actually happened to be right above it in the spritesheet, so you can see that it renders a small part of it.
Now, if I'd go try build a reproducing project of this... I have a feeling I can't... but just in case this is a known problem or similar, maybe it can help someone.
For now I just move that close button out of the spritesheet, and hope that the error just goes away...