A goal in each half from Jose Callejon and Duvan Zapata meant Rafael Benitez's team returned to Naples as joint Group F leaders, while Marseille's chances of progression are incredibly slim having failed to register a point at the halfway stage.
"We think we could have done better, but we lacked focus in some moments, in certain challenges, from a physical point of view when our opponents were on the attack," Baup said on UEFA's official website.
"It cost us the first goal. I changed the system in the second half and we came stronger with our goal."
Andre Ayew's strike four minutes from time set up a grandstand finish but to no avail.
"We are once again disappointed," said the Ghana international. "There is little to add.
"We could have done it. The first half was balanced, but the goal before the break hurt us."
