The Alfresco Mobile app has moved on quite significantly from both FreshDocs and Mobile Workdesk and hence uses more REST APIs on the Repository. It's possible something is tripping the app up, but I'd expect it to be logged on the server. We don't have any open JIRA issues in this area so I'm not sure where your problem lies exactly.
Regarding building from source: make sure the target is "Alfresco" and not "FreshDocs" as both are present in the project file and Xcode tends to default to the latter.
Thanks,
Mike