If you ever merge and still get problems that dont know what they are, I mean not the obvious marks of a diff
<<<<<
....
======
>>>>>>
Then you can analise your project files with https://github.com/Karumi/Kin, install it and use it
kin project.pbxproj
It has make extrange erros that doesn't allow open the project more easy to understand and solve (ones of hashes, groups and so on).
And by the way, this could also be helpful, thought I have not used it try to diff 2 versions of your project files https://github.com/bloomberg/xcdiff so this will give you really what is going on.