I believe this issue was previously highlighted by @LuSanto in a separate post (does q2-cutadapt support dual indexed reads? - #15 by thermokarst). @LuSanto highlighted that the current demux paired-end command ignores the reverse barcode, which when one follows a combinatorial indexing approach, has a tendency to only detect unique forward barcodes. @LuSanto solved this issue by making separate metadata files for each unique forward barcode and demuxing his fastq file multiple times.
I currently have the same issue with my files, but I have so many different barcode combinations that prevent me from using @LuSanto approach. @thermokarst suggested there is an update on q2-cutadapt 2019.10 / cutadapt 2.3 which supports UDI strategies, but the forward and reverse barcodes must be all unique.
Good luck!