Can conventional PCR amplify DNA from different organisms from a specimen in a single step?
If you had a 100% BLAST hit for 3 species from a single amplicon sequence then it only means that region of DNA is conserved in the three species so you have at least one of those species present not necessarily all three.

If you had three different amplicon sequences and each one matched one species to a total of three, then you have all three species present.