Currently, my Codex is showing a notification "!" despite no notifications or new entries in the tab.
I also recently purchased the "Ultimate Map Pack" bundle. I was exploring after and went to obtain an Opal marked on the map. Afterwards, I was killed by a bear and the opal marker reappeared; however. The Opal is not there to pick up and my current count says I have picked it up. The map marker is still there, however, and won't go away.
There is also an issue where I started a new game to remedy these issues, but the new game doesn't have the map pack installed and I can't rebuy the pack because it's not in the store.
I'm not sure if both of these glitches have to do with dying and autosave. I tried deleting the game save data, Uninstalled it from the PS4 and it persists on all counts.