How to determine the specific rule Mail App used to move a given message?
2 ways I can think of, neither particularly 'fun'


The 'one rule' method  


Disable all rules bar one  
put the 'mistreated' email back in the inbox  
Run the single rule  
see if it moves the email  
rinse &amp; repeat

the 'sounds' method  


Add a new line to each existing rule - Play Sound  
repeat for each rule, using a different sound  
move the email back to the inbox &amp; Apply Rules

a late posible 3rd… eliminate by halves [based on 1, but better for a large number of rules]
but this requires that no rule will halt the entire process with "Stop evaluating rules".  


Add a rule halfway down the list that will play a sound if it processes that far.  
test by halves, disabling rules &amp; moving the sound to the 'silent' half each time