I have encountered the same error and find that every time I try to manually download the databases, I get different results. Sometimes the mpa_v30_CHOCOPhlAn_201901.rev.1.bt2/ mpa_v30_CHOCOPhlAn_201901.rev.2.bt2 files are just not included. Sometimes one or more of the file sizes are zero. I have followed another thread (Humann 3 bowtie error - #9 by nasnuvens) that suggested deleting the .bt2 files and manually rebuilding the index. This seemed to work for me but I am not sure if the files are complete.
For someone who has successfully used these databases: what are the final sizes of each file in the metaphlan_databases directory?