Hello
On the picture, she seems OK except the the holes (perharps a caterpilar problem?).
If you give her too much water, then the roots rot and she makes black leaves & she dies.(nerver let the ground always wet) But I dont know if it's your case but 2 leaves are suspicious... For the water, you have to water when Salvia's ground is dry in a depth of average 2cm.
Could you descride the little flies ?
(Sorry for my bad English^^)