Pep Guardiola's side ran riot over the north London club as the registered a 3-0 victory over Arsenal at Wembley in the Carabao Cup final. Days later, the Etihad were successful in repeating the same scoreline when these two teams met in the league.
Aubameyang arrived at Arsenal from Borussia Dortmund in the January transfer window. He started in both the matches for Arsene Wenger's side as he saw the English capital club suffer defeats at the hands of City.
The Gabon international admitted he and his teammates were disappointed with the defeats. Aubameyang even stressed that Arsenal players were unhappy with their displays in the last two fixtures.
"There's a lot of disappointment. I think that this evening it was a match without anything positive," Aubameyang told SFR Sport, as quoted by Goal.com.
"We're not happy with our performance, whether it be Sunday or tonight [Thursday]. As we weren't able to score the goal that might have pushed us forward, we know very well that City play very well.
"They're perhaps the best team in terms of playing style in the world right now, so of course, it's not easy when you can't score that goal, you need to have that extra energy. So, perhaps there were some players who were a bit resigned."
After the latest defeat, Arsenal are sixth in the table with 45 points, 10 points behind fourth place Tottenham Hotspur. Aubameyang admitted the Gunners' best chance of qualifying for next season's Champions League is by winning the Europa League.
"I think obviously the Europa League is a good option to qualify for the Champions League," the ex-Dortmund star was reported as saying by The Sun.
"Now the route is not easy – 10 points from fourth place. It is going to be very hard but he will fight till the end. The championship is not finished – this is the Premier League, anything can happen."