I'd review all settings.
If you created your own CA, did you install Active Directory Certificate Services and then Certificate Authority? Did you install NDES as a role service for ADCS? Did you specify a user with adequate permissions as the user account for NDES, and add them to the IIS_IUSRS group? What key character length did you select? Did you install Certificate Enrollment Web Service and change it to Client certificate authentication instead of Windows Integrated?
Did you configure NDEs to allow multiple uses and non-expiration of the NDES enrollment challenge password by modifying the registry and restarting IIS, then confirming at http://<host>/certsrv/mscep_admin that it can be used multiple times and will not expire?
Have you configured SCEP and the certs? Did you make note of the Subject CN= value which is needed during the configuration process from the Details page of the SCEP certificate? Did you create a new profile in the iOS configuration editor and paste in the proper values (http://<ip address>/CertSrv/mscep/MSCEP.dll)? For the subject, did you remove all spaces from the Subject CN= value? Did you copy the enrollment challenge password from the mscep_admin page and copy it to the challenge phrase within the iOS Configuration Editor?
For the iOS MDM Enrollment profile, did you select the SCEP payload you created above and your subject is in the form com.apple.mgmt.<whatever>, is all lowercase, and matches what's on your APNS certificate that you installed on your MMS server?