I’m having a similar problem where i can’t get any cores to load… I followed the instructions here
https://buildbot.libretro.com/docs/compilation/ios/
I’ve confirmed with this command
codesign -dvv mednafen_psx_libretro_ios.dylib
that the core modules under
libretro-super/retroarch/pkg/apple/iOS/modules/
have been signed.
They appear in the list of cores I can choose from when running retroarch on my iPad Pro but when I select any of them “Load Core” I’m left with (No Core ) displaying in the top menu bar. If i go ahead and try to run a rom then select a core that i’ve loaded i just get the popup at the bottom of the “failed to open libretro” popup at the bottom of the screen.
dayton94, your suggestion of manually signing cores into the modules directory BEFORE building retroarch is something I could look into i guess… Should I clean my build to try your fix out? I’ve built successively and deployed to the pad as the documentation mentions that sometimes they’re signed after they’re copied to the pad so don’t work the first time you build but if you just build and deploy then the 2nd time round the signed versions get written to.
I’m also curious about the 32bit/64bit mixup potential that atsumori-neo has suggested… Not sure how to discover the build type for the cores and retroarch but I’m guessing we all need to be using 64bit soon with the imminent iOS11 requiring it.
Sort of our of ideas at the moment… there’s no debugging obvious in the output from the program when attached to Xcode whenever the cores fail to load 
Any help is really appreciated! Cheers!