My gardenia blossoms have black weevils deep in the blossom. I have to dunk blossoms in water for a time until bugs drown but the blossom is not full and has a dark look.
Bugs in Gardenia Blossom
Certified GKH Gardening Expert
They are actually several bugs tha can affect these plants, though I am leaning towards thrips as they are only on the blossom. All are susceptible to an organic insecticide called neem oil. These articles will help: