Two goals from Jarrod Bowen and one each from Josh Magennis and Kamil Grosicki sunk North End, in a game that the Lilywhites were soundly beaten in.
Neil had depleted numbers to choose from, with a host of players missing Ryan Ledson was forced to drop into right back.
The PNE boss bemoaned the timing of the injuries, as Hull City's strongest players are in the wide areas.
"To start with, we had players playing out of position," Neil explained.
"We had one fit full back at the club, we’re missing a left sided centre back and naturally our defence is weakened because of that.
"It’s difficult because I’ve had to put young Ryan in at right back, which he’s never really played, Hughesy’s been missing most of the season and then Ben Davies is out.
"Tom Clarke is then out, Alan Browne would have played at right back but he’s missing, Darnell is missing and it became difficult.
"It’s one of them where we’re coming up against a team where their best players are the two wide players and all my full backs are missing.
"I knew before the game it was going to be really difficult.
"We spoke about this last season, you can cope with people being missing but when it’s in the same positions next to each other.
"The fact is, the team that started the season – we had one available tonight that started the first game of the season.
"It shows how weakened that area (the defence) was.
"We had lads in there trying their best to get the job done but we found it tough."
PNE were not without their chances in the game, Sean Maguire hit the post with the scores still at 0-0 and Josh Harrop swept one into the woodwork into the second half.
Neil felt his side were a threat but acknowledged the quality that the home side possessed in their forward areas.
"We sat in really deep in the first half because we know they have pace at the top end.
"We had a few opportunities, I thought we looked dangerous going forward.
"First half, we hit the post and we had three great breakaways including that where we got at the full back but we didn’t really have anything at the end of it.
"They looked threatening going the other way.
"They get in behind us for the goal, which is really disappointing, we commit when we don’t need to and the ball gets put in behind.
"Up until that point we had three or four opportunities to get a goal and we didn’t do it.
"Second half, I then change it a little bit, put Ryan to the left and bring Joe over.
"The timing of the goal was horrific really, we give that goal away and then it becomes really tough.
"We try and squeeze up the pitch to force the issue and it leaves space in behind.
"It became really tough.
"One thing I will say, their forward players we struggled to deal with and I thought they were ruthless when they were in good positions."