Due to some changes at NCBI regarding their database structure we have seen disruption with some of the functionality from Geneious.
We are working towards a solution for this, but in the meantime we suggest downloading genomes directly from NCBI's website and importing those into Geneious.
NCBI Genomes can be downloaded in several formats. For easy importing into Geneious with pre-filled metadata, choose fasta and annotation features (GFF or GTF) after selecting your file source (RefSeq or Genbank).
Once you unzip the ncbi_dataset download, you might see both GenBank (GCA) and RefSeq (GCF) folders (unless the file source is specified). Within these folders, find the .fna (fasta) and the .gff (annotation) file and drag these into Geneious to import your complete annotated genome sequence.