While City appear fluent with nine wins on the bounce, United are still untidy at the back and cautious in attack where the luckless Wayne Rooney continues to splutter, even against third-tier opposition.
Mourinho’s team really ought to have killed this cup tie the moment Michael Carrick scored with an elegant strike in the first half.
Yet nothing is quite straightforward at the moment and the well-heeled from Old Trafford were made to stumble in shoe-making country.
Northampton levelled before half-time when panic took hold among United defenders and Daley Blind conceded a penalty which was converted by Alex Revell.
Mourinho was forced to summon Zlatan Ibrahmovic and Marcus Rashford to secure a place in the EFL Cup fourth round.
As ever, Rashford made a difference where others could not, with the teenager involved in the crucial second goal smashed in from the edge of the penalty area by Ander Herrera.
He then scored the third, a simple tap-in after Northampton goalkeeper Adam Smith had made a complete mess of a long punt as he tried to field it on the edge of his box.
“We deserved to win, clearly,’ said Mourinho. “It was difficult, as I expected, but we were totally in control for the first 35 minutes and then the last 45.”
The United boss could not resist the urge to grumble about referee Stuart Atwell for showing Jak McCourt a yellow card and not a red one for a foul on Memphis Depay early in the second half.
Depay did not last long after that. There were bad tackles flying around. Ashley Young and Morgan Schneiderlin were also on the receiving end.
“The game should have been easier because normally it is easier against 10 men and we should been playing against 10 men,” said Mourinho.
“I think I should stop speaking about referee decisions. I spoke about the red card. I am talking about something which could end in a serious injury.”
Three United goals, however, masked another ponderous display and the increasingly uncertain future of Rooney, given a rare chance to start up front but unable to sparkle.
Before kick-off, Mourinho had told the TV audience to expect ‘goals’ from his captain.
Maybe not six, as scored by George Best when the teams last met and United won 8-2 in 1970, but certainly something to boost his confidence. One would have been nice.
It did not start well when he somehow got in the way of an attempt by Carrick and then missed the target with a simple chance from close range.
Rooney was not the worst on the pitch but he is conspicuous and has scored only four in 25 appearances for club and country.