What does “query to referee” in the tracking system of Physical Review Letters imply?
It can mean that there was something problematic about the referee's report.  This can indicate that there is some kind of inconsistency between what the referee says in different parts of the report.  For example, the referee may have provided a very positive written evaluation, but accidentally clicked the box saying "Reject."  If that happens, the editor will naturally ask the referee to clarify what they actually meant.

One other thing it can mean, particularly in connection with a journal like Physical Review Letters, which has selection criteria that require more than just a correct and interesting paper.  If a paper is deemed to be, in fact, correct and interesting, there may still be some additional back-and-forth communication between the editor and referee(s) to ascertain whether the work is important enough for that particular journal.