You probably want to use a sub search that pulls the user id and matches (or NOT) across the other file. To do this:
Create a field extraction for the userid in Log A & B. The field name should be exactly the same in both extractions.
Search for all users that logged into System A and output only the userids. Similar to:
source=Log_A user_logged_in | fields userid
Use the latter search as the subsearch to find log ins for Log B. You must make sure the a field extraction exists for userid in Log B, otherwise the values passed from the subsearch won't match anything. Similar to: