The managers have since patched up their differences, with the Manchester United boss even suggesting they could become friends, and Mourinho feels some of the spats between himself and Wenger over the years crossed the line.
"Looking at the performance and the way the game went, it was the worst possible result for us, but we have to go there in a positive mood and qualify over there".
Mourinho and Wenger have had their fair share of spats throughout the years, while Wenger's relationship with the United fans has also been largely negative.
"There were little things it would obviously be better without - some gestures, some words", Mourinho told reporters ahead of Sunday afternoon's (Monday morning AEST) Premier League game against Arsenal at Old Trafford. I think these great teams Arsenal had, and the fight they had shoulder to shoulder with Manchester United, made Manchester United better and better, so I hope they have that feeling.
But he was always really welcoming and it's always cool to meet our team boss - I've been supporting them since I was five, so I really want to wish him all the best and I think his future is as bright as he wants it to be. "I realise that better at a distance than at the time".More news: Jan Oblak casts doubt on Atletico Madrid future
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Mourinho added: "They pushed us to the limits, the two matches we played, not at the Emirates, but at fantastic old stadium, were unforgettable".
"When I arrived in England 2004, Arsenal was the champion and the famous Invincibles". The only negative thing was Paul [Pogba]'s red card which stopped him from playing in three important matches.
Manchester United squad: De Gea, Pereira, O'Hara, Valencia, Darmian, Shaw, Young, Lindelof, Smalling, Jones, Rojo, Bailly, Matic, Carrick, Pogba, Fellaini, McTominay, Herrera, Mata, Lingard, Martial, Sanchez, Rashford, Lukaku.
Arsene Wenger admits he faces a task lifting his Arsenal players after they were held to a 1-1 draw by 10-man Atletico Madrid in the first leg of their Europa League semi-final on Thursday night. "When I go back I realise what a great team they were".
"Yes, yes, I speak to everyone and yes I met Martin Edwards", Wenger said. Everybody knows that I bought Salah [at Chelsea] with Mr [Roman] Abramovich's money.