Some prior Q&A about this is here: https://www.biostars.org/p/220422/
And the full FAQ for the tool suite is here: https://www.blast2go.com/support/faq
Look under the section "Some of my sequences have low blast e-values and mapping results but failed to get annotated. Why?"
The tool also has a google group (linked from the FAQ) if you need more details not present in the core publication or in prior Q&A.
Thanks, Jen, Galaxy team