It's been claimed Raul Sanllehi was pushed out of Arsenal last week due to the Pepe deal last summer.
But Lopez told Sky Sports: "I think it is made up stuff.
"I know for a fact he has an excellent relationship with the club and they left on excellent terms.
"There are always going to be stories that try to be interesting, Arsenal are going through a restructuring which is part of what happens. He is a great guy, it is a great club and as far as I can see they both [Arsenal and Sanllehi] respect each other immensely.
"They have a player [Pepe] where people forget his age, and the fact he took one season to click within our system and then became the player which we all know.
"He has had a good second half of the season at Arsenal and he is one of the rare players who can make something happen from nothing.
"The more comfortable he gets at the club, the more he will make things happen so I think the best is yet to come."