Hi Ryan, welcome to Community!
When you say "It doesn't seem to be a consistent issue", is the problem restricted to only some users all the time, or are these users sometimes able to find their managers? Do you have it set up so that the users can search through everyone, or a pre-defined list? Also, are you on cloud or server?
You may have encountered a bug- did you already enter a ticket with Atlassian Support?
https://support.atlassian.com/contact/#/
There's also a link in there to check the public jira.atlassian.com where bugs are tracked, so you can also see if others have reported anything related to this.
Hope this helps!
Carolyn
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