The Spaniard admitted that his side lacked intensity during the game and said that conceding the first goal threw them into disarray.
"We lacked defensive intensity when they had scoring opportunities and that is why we conceded," the former Chelsea and Inter Milan coach told reporters.
"I anticipated a different game. We controlled the game but after the goal we clammed up. On the second goal we got the defensive marking wrong - this has happened in too many games now.
"In the first half we should've hurt them with our counter-attacks but, after going behind, we didn't have the intensity and pace to avoid their counters. We lacked the desire to win games a few times this campaign. We must improve in that respect."
The result sees Napoli drop to second in Group I, with Young Boys moving ahead of them on goal difference.