BLAST 16s rDNA: Everything alligns to Bacillus sp
As you guessed in the last sentence, it's hard to answer your question without some more information.

For example, how much of the 16S rRNA gene did you sequence? Most people just sequence the v3-v4 regions which are the most variable, but they only comprise a few hundred bases. Sequencing the entire 1500 bp gene gives more specificity when doing searches, but is also more expensive.

With regards to selection of colonies, do you know from the literature how selective your two different types of media are? We did similar studies with environmental E. coli including several rounds of screening and selection, and you would be surprised how much "junk" we got. If you're isolating from soil, Pseudomonas and Bacillus spp. are going to both be highly prevalent. 

With that in mind, it is not enough to grow on selective media, do one transfer, and call it good. Really, you should have a screening method in addition to your selective media. Maybe some compound that yields fluorescence or a visible change to the surrounding media that you can use to differentiate your target bacteria from contaminants. Once you have your candidates, you need to isolation streak them onto fresh selective media. Then screen again and isolation streak again. Repeat this process 2-3 times, or until you have monomorphic, pure cultures. Only then should you start doing genetic/genomic testing on your isolates.

Hope this helps.