While he admires the talent of the Bundesliga outfit, who finished as runners-up in the tournament last term, Baup feels that the result was harsh on Marseille.
"We knew how good our opponents were – they beat Real Madrid 4-0 in May on the same pitch," Baup said in a press conference. "We wanted to play our game, but 3-0 is still harsh.
"We knew it would be difficult from the moment the draw was made. Arsenal always advance, Borussia Dortmund were runners-up last year and Napoli have built a good team. This is an incredible draw – it is the most difficult section. We aim to be brave in taking our chances and, above all, to try to improve.
"We should learn from such games for the league, but also to come back stronger in Europe. On the plus side, our first half was good as we had more possession than Dortmund. Their second goal, from a free-kick, was a bit weird. All those things make the difference."
Marseille face Paris Saint-Germain in Ligue 1 on Sunday.