Since iOS user enrollment is still in preview, there are some limitations. For application deployment, only the following app types can be deployed on the user enrollment devices. Store apps are not supported currently. Thus, the store apps may not be managed, and can't be removed by the Retire/Delete action.
- User-licensed Volume Purchasing Plan (VPP) apps including custom apps
- Line-of-business (LOB) apps
- Web apps
For more details about Intune actions and options supported with Apple User Enrollment, please click the following link.
http://Intune+actions+and+options+supported+with+Apple+User+Enrollment