It appears when I kill a monster, only the first category of that monster is unlocking. ie spear spiderling but not spear spider, skuldr but not skuldr king. Which apparently denies me experience and info on their weaknesses.

Depends on the foe... some don't have an entry, some do.

 

Lionesses unlock for lions for example, and "Young Bear" give the lore entry and XP of "Bear"

I am going via this list. I killed things on that list but the entry would not be unlocked if there was another monster of the same variety already unlocked. (eg, had shadow bestiary entry but not shade etc) I guess I'll try to replicate it.

have you killed enough of each?

Hmmm... I loaded my endgame save and while there are spider and spiderling, I am indeed missing the Skuldr King aswell, even if I know I murdered it long ago.

 

Didn't check Shadow and Shade, time to reboot the game, but it may just be the Skuldr King entry is bugged at the moment???

 

EDIT: Shadow and Shade are both there.

Edited April 14, 201510 yr by Hassat Hunter

I'm having a problem with every type of enemy right from the beginning, some shadows give progress, some dont. some xaurips give credit, some dont. some oozes give credit, some don't.

What a necro!
It is not a problem, it is done on purpose: not every kill reveal info and give experience for any monsters.

For the details, see here:
https://pillarsofeternity.fandom.com/wiki/Experience_and_advancement?so=search#Bestiary_experience