Last updated November 2nd, 2022 (Hotfix 32.0.13)
After more than 2 years, I don't intend to keep updating this thread further.
Instead I updated the wiki with the bugs I had confirmed: https://warframe.fandom.com/wiki/Codex#Complications
A list of Codex Bugs, scans from Quests that you can't replay, and Old enemies that got removed.
If I'm mistaken somewhere, feel free to correct me. (Google sheet of tables below)
UI bugs and other inconsistencies
Minor visual bugs/typos and inconsistencies in the Codex
Missing Codex Entry:
Missing codex scans from some enemies that have a droptable on warframe.com/droptables , and a few others. (incomplete list)
But in my opinion could stay hidden mostly to not clutter the codex page too much. Being able to reach 100% completion is the main reason of this bugreport.