4th Singularity London: Southwark free quest is the best AP & time-saving location to farm Homunculus Baby. You'll get about 3x Homunculus Baby by spending 190AP. Evil Bone is also dropped.
Here is a list of servants that need Homunculus Baby to perform Ascension and Skill Up.
Rashoumon event (Ibaraki Douji event)
Murder at the Kogetsukan
Inheritance of Glory
Heaven's Feel
Gem Magecraft: Antumbra
Dragon's Meridian
Here's Your Honor
Chocolate Craft Essences
Ereshkigal
Arthur Pendragon(Prototype)
Gorgon
Black Holy Grail (The Black Grail)