Hi @Ilze ,
This is a good question — and not unexpected!
Long story short, SILVA does not actually curate the species-level taxonomy. It curates genus level, and provides the species annotation of the "source organism" given for the sequence in NCBI. In many cases, the "source organism" listed is the host of the organism, not the organism that the DNA belongs to 
QIIME 2 (and RESCRIPt, the software used to make the Q2-compatible database) does not do anything to alter this — it takes the taxonomy that it is given, directly from SILVA.
You can check this directly on the SILVA website to see that this mismatch exists right at the source (e.g., g__Endozoicomonas;s__Acropora_cervicornis).
This is discussed a little more in this tutorial (along with steps for building and filtering the taxonomy yourself, including ways to build a genus-level taxonomy if you want to drop the species labels altogether), as well as the following publication: