Jackson Irvine opened the scoring for the visitors just before the half hour in a poor first half from the Lilywhites.
They were a different side in the opening stages after the break however with Alan Browne’s fine strike levelling things up.
They couldn’t build the 47th-minute equaliser though and Irvine bundled home a corner 10 minutes from time as PNE slipped to back-to-back defeats and 17th in the Championship.
“I wasn’t happy with how we performed in the first half,” said Neil.
“We didn’t really carry much of a threat at all.
“We then changed it and put Ryan Ledson on which made the game more open because we had more players at the top end of the pitch.
“We started the second half really well and got a great goal.
“The disappointing thing after that is that with the way the game was being played, I knew the next goal was probably always going to be the winner and we had chances before they scored.
“And if we take one of those then I think we go on and win the game.
“That’s the difference and the goal we concede is really poor.
“It’s a corner and it looks like we’ve misjudged it, it dips under the bar and gets bundled over the line at the back post.
“They had to work for their first goal but the second is a basic corner into the box.
“I’m frustrated because they scored when we’d played some of our best stuff really.”