Eighth-placed United are now 12 points behind leaders City and 12 ahead of Cardiff City who are in the relegation zone.
"I don't like to lose and speak about this player that was not (here), I don't like that very much but he is important for us in many aspects", Mourinho said of Pogba. 'If we had pushed more we could have got a larger result'.
Make no mistake, Guardiola's champions are a team full of talent; every department is strong and the City squad is deep in every position.
Nuno Espirito Santo's men were matched at a high of [6.6] to win the game and soon had the lead when Ivan Cavaleiro scored from close range, but in the dying minutes substitute Henrikh Mkhitaryan saved the Gunners' blushes to rescue a draw.
"But, of course I prefer the three points today than the record".
Instead, Mourinho rattled off excuse after excuse as United lost for the fourth team in 12 games this season after yet another slow start.
Champions last season with 100 points, City heads into the worldwide break with a two-point lead over Liverpool.
There was something of a response at 2-0 when Anthony Martial converted a penalty but the hosts ensured there was no danger of that turning into a 3-2 win for the away side, as it had done here in April.
Nemanja Matic, Ander Herrera and Marouane Fellaini started in midfield for United and the first two had absolute stinkers in the loss. We made mistakes, we were punished for these mistakes. I go for what I felt, for what I saw in the game.
Three minutes into the second half, Jesse Lingard conceded possession on the halfway line to Fernandinho who set Aguero free on a run to goal.
Gundogan finished off a 44-pass move that dragged United all over the pitch, slotting home five minutes from time.
United scored twice in the closing five minutes to win 2-1 away to Juventus in the Champions League in midweek while City continued their campaign in European club football´s elite tournament with a 6-0 thrashing of Shakhtar Donetsk on Wednesday.
A rather hard run of fixtures for the Red Devils will conclude with an away match against Manchester City in the Premier League.
Dani Alves has said he wants to play in England before he retires and given he's 35 years of old, he's going to have to get his skates on.
Leicester City manager Claude Puel must help his team find a new normality after players and fans paid tribute to late owner Vichai in their first home match since he was killed in a helicopter crash.
"I consider the performance of my team one of mistakes rather than a bad performance", Mourinho said.
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