Hi there @11113! We have seen this issue before in the past, this happens because cutadapt will keep 0-length sequences post trimming and/or demuxing. In 2019.4 we added a new minimum_length parameter to trim-single and trim-paired, which sets the min length to 1 by default (instead of 0). We didn't implement this flag on the demux methods in that plugin though (although, we are just wrapping up the addition for inclusion in the 2019.7 release). In the meantime you could run cutadapt on its own (setting -m 1 when you do that).
Relevant Github issue: Expose --m (min output read length) parameter · Issue #17 · qiime2/q2-cutadapt · GitHub