Ryder Matos and Borja Valero struck in the 86th and 92nd minutes respectively to see Fiorentina to a 2-1 UEFA Europa League win in Romania on Thursday.
Montella was disappointed with his side's display and said Fiorentina were 'far superior' to their Group E opponents.
"This match had many positives and many areas we need to work on, including concentration," Montella told Sky Sport Italia.
"There was the desire to take the initiative but we wasted far too many chances. We are far superior to Pandurii, so we need to work in order to improve."
Juan Cuadrado provided both assists for Fiorentina with crosses from the right after the Colombian had started centrally.
Montella was happy the Arsenal target had an impact after being pushed wide but said Joaquin was his man-of-the-match.
"He (Cuadrado) did well in possession, a little less well without the ball, but it was the first time he was playing there. We know he's much better as a winger," Montella said.
"If I had to choose a player of the match, it'd be Joaquin, as he proved he wanted to win right to the end. Everyone should follow his example.
"Now we will try to beat Sampdoria but there are regrets that we used up more energy than we should've done today."
