In most databases, it’s standard to have multiple reference sequences assigned to the same taxonomic group. Some has to do with problems in modern database construction (we’re often missing resolution we’d like). Sometimes, it has to do with the fact that multiple sequences map to the same “species”. Because taxonomy and phylogeny are hard and don’t always line up. And bacterial sex is weird. And species definitions in bacteria are weird. (And if your database isn’t bacteria, sorry. Phylogeny and taxonomy are still not always related, even in macro-organisms. We’ve been doing morphology for at least a century, but molecular phylogeny is far newer.) But, I digress.
If you’re not comfortable with a shared taxonomic assignment, you could add a descriptive column at the end (probably level 7) that designates different features. HOMD, which contains a mixture of known isolates and OTUs does this, and I think it’s brilliant in a curated database.
I suspect, though, that if you have too many closely related organisms, you may just not be able to distinguish accurately and may ultimately lose the resolution in classification. (I havent bench marked this, its just a hypothesis),
So, tl;dr Multiple unique reference sequences mapping to the same taxonomy is normal and fine.