I noticed this today when we started using ArcGIS Pro more frequently. Several users reported that not all of the features are in Publication. Below on the left is my OS-Auth connection to Publication using ArcCatalog. As you can see, lots of features in there. The one on the right is the same OS-Auth connection to Publication using ArcGIS Pro. As you can see, not so many features in there.
The only difference between the features that do show up in Pro vs. ArcCatalog is the explicit object level permissions. I've got my Active Directory group for my GIS Users and I gave them select rights at the Database level for my Publication database. Some of these features I did happen to go to the feature level (object level) and grant explicit permission to my AD GIS Users group. Those features with explicit object level permissions show up in Pro. It's almost like ArcGIS Pro is not inheriting the database level permissions, and instead looking soley at the object level permissions for each feature class.
This is ArcGIS Pro 2.0.0 ; backend is SQL Server 2012R2.