I just noticed that the order in bdo codex is way different than in game....Why isn't it matched to each other??? It's common sense to do that

Are you asking PA?  lol

I want to bring this stuff to their attention. Like seriously, why isn't it matched!!? I see stuff on bdo codex that isn't in the game...They have different categories, i guess is the right word, and the knowledge doesn't match up. I was doing the log II in game and on bdo codex, there was stuff under log II but in game it was under log V or something

You should ask, why official website and developers didnt bring to people so great and useful options like bdo codex, bdo lytics, garmoth. These sites arose precisely because the developers did not.

some stuff in bdo codex I don't even see in game....there's more catagories

The game doesn't show a category until you get at least one entry in it.

First off, use bdolytics.  Most of the knowledge is in order.  Second, any that say "unobtainable" (most anyway) you need to get by reading pearl shop bookshelves. 

Good luck.

Bdocodex, Bdolytics, garmoth.com, etc are not official resources. They all use either third party data gained through testing and experimentation, or through data leaks / reading launcher data. But not everything that is added to the game files (which is what is in the databases maintained by bdolytics and bdocodex) is also in game, simply because the devs have not decided to enable it yet or for other reasons. If you have an issue about something on codex not following what is in game, send the creator of it a message (he responds pretty quickly to discord messages btw) and they might fix it. PA themselves have nothing to do with these third party websites though, so complaining about it here has no merit.