If you have a Maven artifacts in Nexus 2 whose artifact ID does not match the ID of the artifact folder they reside in these artifacts will not be migrated to Nexus 3 on upgrade.
See attached screenshots for an example of this.
This is a critical bug, it is unfortunately not at all uncommon for users who are running Nexus 2.x on Windows to have artifacts whose case changes over time. These will be lost on upgrade.
I've attached the work directory from Nexus 2.x to make this easy to reproduce.