Choose your tool
If you have installed ag and not rg then ag will be used according to the documentation string in your dotfile you can see that Spacemacs tries the search tool in this order first rg, then ag, pt, ack and finally grep.
Hack your tool
One solution is to use the options of the tool you are using in your case for ag:
create a .agignore ignore ...
The answer provided by Magnap didn't work for me, and neither did the accepted answer of this apparent duplicate: Use Helm for Org Refile Completion
What finally worked was this answer: How to get helm completion for an arbitrary function such as dired or magit-branch?
Just adding: (helm-mode) (I had previously been using helm only for specific things)