In-vitro microbial kill rate study [Study Assessment]
this is a failed trial, and there is little reason to submit in the present form, it will most likely be rejected.
However, you do have data strongly indicating that your product is not bioinequivalent. I think your problem is very likely a lack of power for the fungi.
It is probably this sentence that got you into trouble: "The in vitro microbial kill rate study should be conducted by using at least 12 replicates for each kill rate study of each organism." I guess you never really went into the "at least" part
You need to send a quick controlled correspondence to FDA and argue that it is lack of power that is your problem (not lack of BE, you just failed to show BE at your current sample size), and try to convince them that a repeat trial on some or all of the organisms with increased sample size is necessary and justified (you will need to discuss type I errors and more, rather than focusing only on bacteriology and mycology). Await their response and do exactly what they tell you.
Good luck. Please post here what you decide to do and what the outcome is.
I could be wrong, but...