It's possible (though I haven't fully investigated it) that some regions may be missed if they were not initially loaded. I don't think this will cause trouble since normally a player will be near the region they need, but it may cause issues. Or it might be that regions are already loaded and this is a non-issue.
Polygonal regions may not be handled precisely
Chunk overrides are not updated when regions are, since WorldGuard does not create any events for that. Players will need to manually refresh their permissions for changes to take effect.