So, we haven't encountered this since we switched to 5.5. But when I setup a imodel in 5.5, the imodel displayed meshes that shouldn't be displayed at that moment in time. This is using ItwinTemplate running in 5.3 and 5.5 with no special settings. Just running in 5.3 and 5.5. They're purely that ITwinTemplate project under 5.3 and 5.5 with identical app ids, model ids, and changeset ids.
I can add people to the imodel if needed.