The visitors had started the brighter team and created several good openings, but they failed to take advantage and were made to pay as the Magpies went ahead against the run of play.
The hosts were clinical in their finishing from there on as they leap-frogged Crewe in the Sky Bet League One table, with 20-year-old winger Callum McGregor, on loan from Celtic, scoring two of their four goals.
Davis said: "It's how it goes sometimes - when you're down you don't get much. But I'd like to see the stats throughout the game because we probably had more shots on target.
"The possession wouldn't have been much different as a lot of theirs was very deep in their own half and I thought that we played reasonably well.
"It was a much better performance than last week against Gillingham and there are positives to take out of it.
"If you were a neutral looking at the result and you hadn't been here, you'd think that we had been thrashed. But if you were here, you would have been encouraged with the performance."
Had Crewe struck first at a time when they were on top, it could have been them celebrating their second win of the season and not the hosts.
Davis knew as much and admitted it would have meant a much different game, saying: "It counts for any game because opening the scoring allows you to settle into the game.
"If you get that early goal, it allows you to defend and hold on to your lead and build on it.
"We had two or three great chances early on where Max (Clayton) blasted one over, we had a couple of shots wide and their keeper has made a couple of saves where he's parried it but we couldn't get to the rebound.
"But that's the way it goes and obviously we're disappointed with the result, but encouraged by the performance and it gives us something to build on."
- Sports & Recreation