The French coach talked of frustration after his side failed to score in their last match, although he is glad they are included in today's group stage draw
After winning 2-1 in Moldova, the current Ligue 1 leaders were expected to widen their aggregate lead during the home leg to cement their place in the next round, however the game turned out differently than expected.
"There is a disappointment because we created a lot of chances and did not score," admitted Baup, speaking to FranceFootball.fr.
"Our game is to score and if you do not, you are put [the result] at risk. But it sees us qualified.
"They stayed in the idea of the first game, but it was us who couldn't separate ourselves from them."
Loic Remy, who has been linked with a deadline day move to Tottenham, spoke positively of his own performance.
"I found my thrill, my calling, my races. Tonight was not easy, as we expected, but the qualification is still there," said the 25-year-old forward.
Attacking midfielder Andre Ayew remains optimistic of their chances of a good season, despite the prospect of losing some key players.
"It is difficult to lose a player like Stephane [M'bia], it's hard to swallow, but our leaders must do whatever it takes," conceded the Ghanaian.
"We must continue like this until we all pull in the same direction, it's okay. There is a match on Sunday against Rennes, it will not be easy."