According to here: http://paizo.com/pathfinderRPG/prd/monsters/creatureTypes.html most creature types are proficient in the weapons they are described as using in their entries. I have found the following monsters that are lacking proficiency in the weapons they are described as using:
Atomie rapier
Baykok- longbow/composite longbow
Clockwork Servant- Net
Clockwork Soldier- all simple and martial weapons
Cold Rider- glaive
Cyclops (Great) Greatclub
Derhii Falchion
Faun Shortbow
Giant (Cave): Battleaxe
Giant (Desert): Scimitar
Giant (Jungle) Longbow/Composite Longbow
Humbaba: Longsword
Kech: Longbow
Maftet: Scimitar
Nixie: Sword (Short)
Norn: Scimitar (This is what the shears are treated as)
Pale Stranger: Pistol
Sprite: Sword (Short)
Terra-cotta soldier: Longsword, Sword (Short)
Thriae Soldier: Longbow/Composite Longbow
Completed: At revision: 25502
The following are still missing:
Derhii- Falchion
Faun- Shortbow
All others seem to be working.
#25506