I probably should tone it down a bit on this, so let me explain rationally. Farrell's budies in Cleveland basically have said that Farrell was treated badly.
Putting it all together we have comments from Farrell regarding hiring his Boston hitting coach, comments from Lind regarding Farrell vs. Murphy, comments from Farrell regarding "Player development", long standing comments from Beeston/Gaston/Murphy regarding philosaphy on player development and hitting approach (old is good, pull is good, opfield is bad, oba is bad).
My guess is Farrell wanted an on base ish team and had a lot of thoughts on player development. Cito still has Beeston's ear so Beeston basically thought the opposite of Farrell. AA was really hired to implement Beeston's vision (starting with a year long retirement ceramony for Cito) so AA is powerless.
Beeston didn't like or listen to Farrell, and thus the reported tension extended to AA and Farrell (AAs is only there to fulfill Beeston's wishes, like anybody has to for their boss).
In the end Farrell didn't get screwed, got his dream job and won the World Series. It would be more accurate to say that Beeston and Farrell did not see eye to eye, Beeston didn't take Farrell's ideas seriously.... Farrell in the end went to be part of a team where everybody was on the same page.