This is happening because you likely have a huge amount of legend options (most probably with long names) and this is overshadowing the plot itself. You should try filtering the number of samples that you look at when you go to lower taxonomic levels or only look at a subset of taxa. For example, instead of looking at all genera in your dataset, try to look only at the genera that are present in your most abundant phyla.
Even if you could fix the legend issue, your abundance plots would likely be impossible to interpret because of the large number of individual taxonomic assignments and the limitations on discrete color distinction.
You should take a look at filter_taxa, subset_taxa, and subset_samples (and other similar functions in the phyloseq package) functions
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