The Black Cats laboured in the first half, with Bailey Wright's error allowing the visitors to take the lead.
It was one of multiple errors in possession, and at half time the host's play-off aspirations looked to be hanging by a thread.
Neil made two changes at the break, switching to a very aggressive system that saw Lynden Gooch and Jack Clarke operating as wing backs.
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Despite that, Neil admitted the scale of the problems in that first 45 meant he wasn't able to take much satisfaction from the win.
"I've been saying for the last few weeks, it doesn't matter what the game is, we want to subtract the performance from the result," Neil said.
"The result was excellent, the performance was extremely poor. We won't hide away from that, the lads know that.
"We fell well short of our standards, however what we had to do was find a way in the second half to win the match.
"Teams who win titles and get promoted don't play well every week, but they find a way.
"Fortunately enough for us, we managed to do that.
"But to be honest, I'll go home tonight and it feels like a back to the drawing board for me.
"I don't want to put a dampener on a win, but I don't take massive satisfaction from that at all."
Neil said the issues in the first half were a combination of his side's errors, and a smart gameplan from Stephen Crainey's Fleetwood side.
The head coach admitted that his half-time changes, which left his side vulnerable to the counter-attack, were a big risk.
"I think you've got to give Fleetwood a lot of credit," Neil said.
"I saw their coaching staff there and gave them credit for what they did, the young lads who worked really hard made it difficult for us.
"They left our centre halves on the ball, we found it difficult to play through. We forced it when we didn't need to, and they sat in and hit us on the transition. That's exactly what I would have done if I was them, so fair play to them.
"At half time, I didn't even talk about the first half. I said, 'put that to bed, this is how we fix it'. I changed the shape, played a 3-5-2 with wingers at wing-back, but we didn't stand up against their full backs so they have to come searching for them, and that leaves space in behind.
"We needed to move the ball quicker, commit more people forward.
"It meant defending 1-v-1, so it's a high-risk strategy. It was either going to win us the game or it wasn't, and I wasn't going to get beat by one more goal, and then would have been a hell of a lot of noise at the end."
"You can't legislate for some of the mistakes we made in the first half," Neil added.
"What I'll say to the players is performances will dip and peak, as long as you try to do what I ask you to do I've no issues.
"Unfortunately, for 45 minutes we didn't reach near out standards. And listen, the lads are very aware of that.
"I was tempted to change it before half-time and to be honest I normally would, but the difficulty with this group is that we've not worked long enough together for them to understand what I need of them without getting them together.
"So I needed to wait for half time.
"The one thing I said when I came here, and I've done it everywhere I've been, I'll risk losing a game to win it.
"If it costs us matches, then [so be it], but with the group we've got I believe more often than not it'll fall in our favour.
"We went for it, we understand the dynamic and what we need.
"And I will point out, it won't always work."
Fleetwood boss Crainey said he was proud of his players and that the result was not a reflection of the game.
"I just said to the group in there, I’m absolutely gutted for them because I thought on the night, we were outstanding," Crainey said.
"I know we lost the game 3-1, but it’s not a reflection of the game at all for me.
“I thought we were comfortable in the lead up to Sunderland’s first goal. We were really comfortable at that point but unfortunately, we didn’t get anything out of the game.
“If we keep performing like that, we’re going to be absolutely fine I’ve got no doubt about that.
"We’re losing games of football, we need to start winning games of football, but the character in the dressing room is big and that will see us alright in the end.
"We’ve got a top group of young players at the club, and they went and showcased their talent tonight yet again against a good Sunderland side who will be there or thereabouts at the end of the season.
“It’s not just the younger players, it’s the senior players as well. They helped them and guided them through the game, so as a collective it was a good performance but really disappointed not to get anything out of the game.”