Hi @SandraQ2,
Indeed, this sounds like an issue with adapting the classify-consensus-vsearch classifier for the functional gene you are working with. I recommend modifying some of the parameters to see how this changes your results — this is more or less the answer to the question posed in the title of your topic. if you have a mock community or other test data to work with it would be ideal for guiding your selections.
Great! Probably due to the better resolution of your marker gene
Could be a parameter issue, e.g., see the perc-identity and query-cov parameters.
Or could be a database issue, e.g., if the species in the database do not encompass all species you are detecting.
Or it could be an issue with non-target DNA! I recommend reading some of the archival topics on this forum for more details on troubleshooting unclassified features... see Frequent Questions and "Best of the QIIME 2 Forum"
Please let us know what you find!