Carboni was on Benitez's staff while the former Liverpool manager was in charge at Inter this season.
Asked about Benitez's departure, he told TMW: "Yes, the idea was: either we change route or a divorce would become natural.
"We pulled out due to problems inside. Believe me, both I and Benitez have no grudge against Inter. I often hear from Rafa and he has no pebble in his shoes for them."
Asked if Benitez will return to Serie A, Carboni added: "Who knows? His resume is not inferior to the Italian coaches that are here now."