Alex Morris says the controversial end to the 2-2 draw with Northampton does not tarnish a good start to the 2022-23 season.
Crewe led 2-0 thanks to a Courtney Baker-Richardson brace, but a Sam Hoskins double snatched a point for Town.
His second came in the 98th minute, after referee David Webb had only signalled six additional minutes at Mornflake Stadium.
That sparked anger from Alex fans, but the manager said 10 points from 15 still represents a strong start.
Morris said: “Two points have been taken away, but you can’t take away the positives from the performance.
“Yes, the opposition had more of the ball than we did in the second half, but we are playing one of the best teams in this league.
"We are not the completed article, far from it, and these lads have shown pride, energy and effort into getting wins for this club. It’s still been a good start to the season.”
The boss admitted he had been left baffled by Webb’s explanation for the extra time he allowed, which gave the visitors chance to take two corners.
He added: “The goal was scored after 7mins 30secs of added on time, and the referee had given six minutes.
“The referee said the reason an extra 1min 30secs had been added on was because he booked Dan Agyei and Lee Burge. So that took 1min 30secs apparently! Obviously, that wasn’t the case in reality.
“Decisions like that change the whole week for people. We’ve got 4,000 people going home now absolutely gutted, rather than jubilant at another win.
“The lads have invested a lot of energy into their performances and staff have invested a lot of time into planning, and we’ve had it taken away through a decision out of our control.”