The Allianz Riviera hosts found themselves a goal down on 12 minutes when Mateo Pavlovic scored ahead of a 34th minute second from Karl Toko Ekambi.
But Mario Balotelli pulled a goal back from the penalty spot on 39 minutes ahead of an own-goal on 76 minutes by Ismael Traore.
Speaking after the match, Favre told the club’s official website: “We had a very difficult start.
“We were too rushed, far too much through the middle, because they were well grouped, very compact, a kind of 5-4-1 which got going quickly at the breakdown, and that’s where we made lots of errors.
“We gave them easy balls, we played too centrally and it was being countered very quickly.
“I always say that when we attack, we need to think about defending, and when we defend, we need to think about attacking. And there, in the transition between attack and defence, it wasn’t great. We knew that they were dangerous.”
He added: “They defended well and went quickly on the counter. It is positive that we came back. At the end, we could have got it to 3-2, that would have been brilliant.
“But it’s already positive that we came back given how we started.”