Hi @emmzee,
One other thought, assuming it is not contamination or whatever, you may have to look into blocking primers to limit off-targets. We had some varying success using this approach with feral swine, i.e. blocking ~5-45% host COI. I'll go ahead and shamelessly plug this paper too, just so you can see how we approached some other odd findings.
Any-who, leveraging peptide nucleic acid (PNA) is another option. We used this approach for one plant-microbiome study I was involved with, we cut down the plant-host 16S rRNA gene sequences by 50%-80% and greatly increased our access to the microbiota.
Either of these approaches may help with blocking common off-targets. Most of the time people just construct a blocking primer / PNA to inhibit the most common read they get from their pilot sequencing runs... and hope it works. 
Best of luck! Please do keep us posted. Hopefully others will qiime-in. 
-Mike