Oh, I see. OTUs which are not present in greater than --p-otu-thresh fraction of samples get converted to NaNs. This is not a bug, this is the expected behavior of the plugin.
I recommend keeping the behavior as is, and just removing the OTUs which are NaN before your next analysis step. Note that even though sparse OTUs aren't converted to NaN when you use --p-otu-thresh, they are essentially converted to noise. So if you use these in downstream steps, they will in the best case be just noise and in the worst case introduce spurious signal to your analyses. Again, check out the previous post I linked for more discussion about this.
Let me know if you have any other questions!