The Frenchman is concerned that the Spain playmaker will be able to play against Chelsea's title rivals when he joins Manchester United, but not against the Blues.
However, Mourinho is not concerned.
"Wenger complaining is normal because he always does. It's something we know," he told reporters. "If Wenger sold [Mesut] Ozil to Man United I would be very happy because they lose a good player, but Wenger will complain and say it's not fair.
"When he says this is not fair I think what's not fair is his team always has the best days to play. When you go to the fixtures during the season, it's never fair because [Arsenal] always get the right times to play, to rest."
Mata had been scheduled to wrap up the deal on Thursday, but Chelsea's negotiations for Mohamed Salah, and poor weather conditions, delayed proceedings.