Les Phoceens now sit bottom of Group F without a point from three matches, while the Italian outfit, along with Arsenal and Borussia Dortmund, have six points at the head of the table
"When you lose, you can consider that you might have done much better," Baup told reporters. "The first half was quite even. Unfortunately some players went missing at certain moments, on the counter-attack or in the move that led to us going 1-0 down.
"We needed to show our face at the back, focus for the full 90 minutes. Mathematically, there are still nine points available and we are fourth with no points.
"It is a complex and difficult situation with two away matches to come. But we knew from the beginning that it would be difficult. You need to measure the capability of our opponents. Arsenal and Dortmund have quality, experienced players."
However, Baup is confident that his players will recover from the defeat.
"This is a difficult period in which few results are going our way but tonight the whole dressing room is readying itself for the games to come," he added.
"The next one is on Saturday and we will not have time to ask questions. We need to look at what went well and quickly focus on the next match.
"I understand the reaction of the fans. We are trying to do the best we can and we need to take points on Saturday against Reims."
Marseille host Reims in Ligue 1 on Saturday.