UPDATE (Nov 29th) - This issue has been fixed in the latest patches for R10 (10.0.6) and R9 (9.1.7).
The NCBI has now begun phasing out sequence GIs which has caused some downloads in Geneious to stop working. NCBI Search itself is still functional, but downloading WGS sequences or full sequences from the Nucleotide service causes Geneious to display an error.
We apologize for any inconvenience this causes.
If there is no patch available for your version, you will need to download sequences from the NCBI website and import them into Geneious or consider upgrading.