Bullet resistant material is not the same as knife resistance for those geniuses out there.
The first lines here contain a description of such equipments and they sound pretty similar to those worn by Batman:
[on ballistic vest]: "Metal or ceramic plates can be used with a soft vest, providing additional protection from rifle rounds, and metallic components or tightly woven fiber layers can give soft armor resistance to stab and slash attacks from knives and similar close-quarter weapons."
It seems to me that Batman was using a soft vest with metal or ceramic plates, without the other fiber for mobility reasons.
Getting stabbed hurts, that is why he was in pain. Common sense thrown in for fun, one can see she was an experience assassin, so she would have known where to hit for it not to be deadly.