We see two cases so far, which has been discussed in this thread: https://social.technet.microsoft.com/Forums/Lync/en-US/55a985c0-e13e-4e60-8561-f5555914e7c8/unable-to-install-intune-company-portal-in-ios-1121?forum=microsoftintuneprod
On the device open up Settings -> Safari -> Block Cookies -> Make sure that is set to not block any cookies. As soon as we allowed cookies the device was able to enroll without any issue.
When the mobile user has this: 
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