I have seen all sorts of levels — it varies by experiment so I can't really comment on how frequently it really occurs but it certainly is a more prevalent problem than many would like to believe. However, it is also probably only problematic with low-biomass samples (as I'm imagining your samples may be, depending on the biopsy site).
Indeed, this would be useful information to have.
Good luck with the next steps! If you are willing to share, please post your findings back here, I will be interested to hear what you find. (and of course please open a new forum thread if you run into any questions/issues with qiime2)