I'm having the same issue with two layers in a service, publishing through Pro from and SDE geodatabase. Other layers in the map from another SDE publish just fine. The problem is with AGOL. All features show up when publishing from the same map to Portal.
After trying a new SDE and a FGDB, I finally resorted to exporting the errant layers to the GDB maintained by Pro for the project. That publishes correctly. Will be a pain to maintain because edits will have to be copied to the Pro GDB every time in order to keep the public app up to date.