Geneious Prime checks your database periodically for erroneous files. Some syncing services (e.g. Dropbox, OneDrive) will create copies of your files with similar extensions while syncing. We strongly discourage the use of syncing services to store your database because it can lead to corruption, which is why you might see this error.
If you do not use syncing services and still see this error, it may be caused by MacOS if you are using exFAT formatting on your external HDD. The exFAT format does not support macOS extended attributes natively, so macOS creates these '._' files to store the metadata. Geneious does not expect to see these extra files (which can also be caused by syncing software) and reports this error.
Formatting your external HDD with APFS should solve this issue.