i’m pretty sure pearl’s defectiveness is the fact she is able to feel any emotions at all. i believe pearls are designed to be cold and calculating, elegant and effective workers. and somehow this pearl came out feeling things - or even learned how to feel things when in contact with rose, who is sweet and cries and cares about everything.

that would explain why she doesn’t have the best interpersonal relationships (to say the least): perhaps empathy doesn’t come naturally to her and she doesn’t fully understand how emotions work. 

this would also explain how jasper even knew about her defectiveness: unless it was a drastic physical change that could be noticed at first glance (and then what could it be? it would be something that is considered a flaw, and she looks fine) then it has to be something in her personality. and that also isn’t something that can be noticed on sight, BUT! if pearls were meant to be essentially robots, and this one left her stations to fight for the rebellion because she fell in love, then news of that would certainly get around. 

maybe the way holo pearls act isn’t even just because it’s a training hologram- but because that is how regular pearls are.