I'll briefly mention that this isn't an error, it's not even really a warning. The Advisor tab is meant to make broad and generic performance suggestions that are meant to guide you towards optimizing your system. Having some of these suggestions that aren't fixable or don't apply to your situation is pretty normal. In fact, my test system gives the same advice about the join without an index.
As Rick James alluded to, these queries might not come directly from code that you write...some administrative tasks may be triggering it (your operating system might run some housekeeping queries, MySQL runs some queries against itself, etc).
The best way to look at the queries is to log them, which is answered in Log all queries in mysql. You could use the "Process" sub tab of the "Status" area in phpMyAdmin (very similar to how you get to the Advisor tab) to look at active queries, but that's not going to give you a complete picture over time. Once you have that list of queries, you can analyze them to determine if there are improvements you can make to the code.