Let's take a look at this step:
qiime vsearch join-pairs --i-demultiplexed-seqs 02_analyses/seqs/paired.qza --o-joined-sequences 02_analyses/demux/demux-joined.qza.
--verbose setting, and rerun that step, and post the new data --verbose provides. That will give us more diagnostic data about how well joining worked, as shown in the example data I posted.
We can also look at the quality of the joinined reads using FastQC or
qiime demux summarize, but that vsearch log will give us the best clues!