England stars Lampard and Cole were reportedly angry at being left out of the line-up for the last-16 first leg, fuelling speculation of a growing rift between Blues boss Villas-Boas and members of his squad.
Villas-Boas admitted Lampard and Cole disagreed with his decision and that debate over his relationship with senior players - as well as the security of his job - was inevitable.
He said: "I think there's a normal creation of opinion from different parties, from the media and the fans, and from exactly the people who matter in the business - the owner and the manager. Whatever perspective comes out, that really doesn't matter to me."
He added: "I had a conversation with Ashley and Frank. The players that they are and the players with the experience they have, they felt they could have helped the team. That's perfectly understandable.
"Of course, they were disappointed but they were decisions they have to accept and move on."