I've only come across it a couple times. Likely the reference ID in the game coding is incorrect.
In the codex, new entries for most things have a light orange diamond in the top right of the picture. Unfortunately that color blends in to most of the backgrounds, and was a poor choice. So you have to slowly scan the pictures for those diamonds to see which are the new entries. The diamonds to very slightly stick up over the top edge of the background, so that is probably the place to look as you scan the entries. If there is a diamond beside the section name it means there are new unread entries in the codex.
But yes, it would be nice if they filtered to the top, or had a glow around the entry, or anything but what they chose. I almost only go in to read the entry once, and only when its new. All the other entries are just in the way once I've read them once. And unfortunately the letters and notes don't highlight as new. They are automatically read because they display when you first find them. Those are the only ones that need to be checked out multiple times, for searching for hidden treasure. Would have been nice to be able to tag them for easy reference.
