This answer can be complicated and due to several variables.
The first is cross-contamination from other samples. Although the chances of this happening are slim, it does happen on occasion. Because samples are run with multiple other samples, it is possible that DNA from one sample contaminated your sample, though we take many precautions to avoid this, and can generally weed out contamination after the fact.
The second is that our libraries are not complete. For example, there are around 1300 fish species in the United States, but only about 500 of these are sequenced an in our library. When there is not a species match to a sequence, the sequence will often match to a closely related species. Oftentimes, this species is closely related, but may not occur within the same system. Typically we can pick out which species it is supposed to be by looking at both closely related species and what has previously been documented in the system.
We are constantly updating our libraries as we try to streamline our methods and as we are able to sequence out more fish species, all of this will become more and more clear.
Please contact us to talk more about this topic.