Emagee,
The reason you get that warning is that your web map may contain elements such as bookmarks, slide shows, etc that are not honored by the ArcGIS app for iOS. Most of these elements are specific to ArcGIS Explorer Online.
Having said that, you should be able to work with the web map even after receiving that warning. The ArcGIS app for iOS will ignore the elements it does not support, and let you work with the layers, tasks, etc in the web map.
What version of the app are you using? And what happens after you receive that warning? Does the app stop responding?