And it came to a head when Ayesteran walked out on Thursday.
Boss Benitez was furious when he saw Ayesteran hugging Mourinho and joking after the Londoners had pinched a point through Frank Lampard's controversial penalty.
An Anfield insider said: "That was about the last straw for Rafa.
"Everyone knows Mourinho is not his favourite person and when he saw Pako showing such affection towards him he saw that as blatant disloyalty.
"There has always been friction between Benitez and Mourinho and Rafa did not take too kindly to one of his staff joking with the opposition manager - especially as he felt Liverpool had been robbed of victory."