Problem with branching and merging is that graphics files might change physical location. Xcode won't complain anything at all, as long as it can find some copy of the file.
Check if you have several copies of same file e.g. under project root and inside classes folder. Find out which one is being used, remove the other one(s) and fix version control to contain only one copy of the file.
Agree common location for all graphics files, regardless if they are used only within one of several modules in project.