Strikes from Shkodran Mustafi and Alexis Sanchez consigned Pochettino to his first defeat in a north London derby, but the first goal in particular drew the Argentine's ire.
Davinson Sanchez was penalised for a foul on namesake Alexis. Although he appeared to win the ball, referee Mike Dean indicated it was for a shirt pull in the challenge.
Goalscorer Mustafi then appeared offside when man-of-the-match Mesut Ozil delivered a free-kick, with Pochettino also uncertain whether Alexandre Lacazette was onside before assisting the Gunners' second.
"The [awarding of the] free-kick [was wrong] and I think it's offside," Pochettino told Sky Sports.
"The first [goal], sure it's obvious and the second one maybe. But in this type of game when you play a team in the top six like Arsenal, the small details change the game and of course put the game in one side.
"This disappointed me but it's football. We need to accept sometimes it's against you."
Harry Kane and Dele Alli played for Spurs, having recovered from injuries that ruled them out of the international break, but both turned in sluggish performances before being replaced by Fernando Llorente and Son Heung-min with 15 minutes to go.
"They were OK to play," Pochettino said. "Of course, after 2-0 with 15 minutes to finish the game I think to take a risk is not necessary.
"We put Llorente and Son on fresh to score and we had chances. Dele Alli and Harry Kane, after 75 minutes, was enough for them."