I have a plugin I have developed which has a custom framework (the plugin works fine, etc. and if I run it outside of the CLI, no problems).
I have created plugin.xml to reflect all custom attributes which I need, and one of those tags in plugin.xml is:
<framework src="src/ios/myframework.framework" custom="true">
And this works fine when adding it etc.
I cannot be sure of the steps to replicate exactly. But somewhere along the line, the directory become corrupted (as far as I am aware, through no fault of my own) and as a result, Cordova is not building correctly unless I manually add in the framework into Xcode (which is not ideal) - so that my source file can compile.
I can provide you with my project - however my code is confidential so I would need to liaise with a Cordova contributor directly.
If not, I can follow some debugging instructions to ascertain, but I have not figured out which script handles the plugin.xml parsing.