Most of Moira's weaknesses are personality. Anyway, here are functional ones I can think of.
Very vulnerable to lightning/ion attacks etc. because droid. Moreover, she does not understand how the Force works. It's something she can observe the effects of and develop countermeasures against its users, but no quantify, meaning while fighting forcers she can be left unable to sense potential dangers. I imagine battering ramming her with TK would work.
Also her imitation of an organic is not perfect - for one forcers strong on perception would see through it. Lack of internal emotion, no Force presence. Moreover, while she looks and can act human, she is not, and that inherent wrongness always shines through in some manner. Like in her utter lack of empathy.