Make no mistake, the big picture remains positive. Toronto (7-6-5) is headed for its best ever season and first trip to the playoffs. The roster and team culture have been smartly remade.
But injuries and suspensions have made it difficult to find the right mix of pieces to complete the puzzle.
And mentally, Toronto has yet to show that it can kill off a game on a regular basis when it has its foot on the other team's neck.
The officiating stole many of the headlines in Saturday's 2-1 loss to Sporting Kansas City, but the inability to finish and some sloppy defending cost Toronto more than the decision-making of referee Ted Unkel.
"Two very soft goals and we haven't got our balance right yet in that midfield," said Nelsen. "Maybe (we were) missing a couple of key players, but our balance wasn't right on the two goals. We were spectators. In a time when we had to be urgent and our intensity had to be focused, we just hoped somebody would do their job and that was unfortunate."
Sadly soft goals have been a common theme of late, with the backline losing its shape and getting punished.
Toronto was missing star striker Jermain Defoe (suspension), captain/centre back Steven Caldwell and right back Mark Bloom (knee) against the MLS champions.
Defoe will be back when Toronto kicks off its road trip against D.C. United (10-5-4) but Toronto will be without centre back Doneil Henry on Wednesday due to accumulation of yellow cards.
Toronto then plays at Montreal, Columbus and Kansas City.
Toronto's defenders were all over the place on Kansas City's goals (in the 48th minute by Graham Zusi and 80th by former TFC midfielder Jacob Peterson).
Brazilian winger Jackson had opened the scoring for Toronto in the 16th minute.
Kansas City players flooded into the penalty box on the first goal by the visitors, with the ball eventually ricocheting back to Zusi who curled it into the top of the goal with Joe Bendik stranded out of position.
On the second, Toronto was unable to defend a deflected cross and Kansas City forward Dom Dwyer flicked the ball back to Peterson, who beat Bendik from close range.
Nelsen complained some of his players had settled for spots that would have worked out well had their teammates won the ball back. But they did not.
"They were some guys that were spectating and getting into nice comfortable position but weren't influencing the game, they weren't helping out their teammates," he said.
"That's a hardness that we lost, I think," he added, "(and) that we need to get back."
Nelsen played a midfield of Jackson, Michael Bradley, Collen Warner and Dominic Oduro against Kansas City, Oduro terrorized the KC defence and Jackson, making a terrific run to take advantage of a marvellous Oduro pass that split the defence, scored one goal and could have had three on the night.
But the Brazilian winger was one player who seemed to be lying in wait for a possible counter-attack on one of the Kansas City goals. And Oduro's mind set is offence not defence.
On a micro level, Nelsen's frustration Saturday was that his team got it right for most of the game other than two lapses of concentration.
On a larger level, he sees a good team unable yet to take the final step to becoming a very good one.
"But this is why it's such a great game," he said. "Nothing is given to you here, is it. You've got to keep working, take little steps, little steps, little steps and eventually these results will go your way and you'll learn from your mistakes.
"We've got some young guys, we had a couple of young players out in the backline. We've still got some new players coming into the team. I feel bad for the guys, because we are very close."
Nelsen saw plenty of positives, which perhaps made the loss more upsetting.
"Our transition was just brilliant today. We absolutely destroyed them today on it."
The pace of Oduro and Jackson, coupled with fine passing from Bradley and others did rip Kansas City apart repeatedly.
"The bottom line is that on too many days we're the team not coming away with points," said Bradley. "Over the course of a season, these games add up and mean that you're not in the position we should be. So we've to take a long hard look at ourselves at the moment and really find a way to translate at times good play and dominating games and turn that into points and wins."
The league will no doubt review Saturday's officiating and the comments that followed.
"It's by no means an excuse, it was the same for both teams, but the referee was absolutely awful," Bradley said after carefully choosing his words. "The people at the MLS (head) office in New York, when they talk about wanting to improve the league, the first thing that needs to be improved is the refereeing, bottom line.
"That shouldn't come across as sour grapes because that's just the reality. And it was bad for both teams and I'm sure they're sitting in their locker-room saying the same thing to themselves but they've got three points with them and that certainly makes it a little easier to swallow."
Unkel issued eight yellow cards, including five to Toronto. Kansas City was reduced to 10 men in the 75th minute when captain/defender Matt Besler got a second yellow.
Foremost on Toronto's list of complaints was a no-call in the 23rd minute when Unkel waved play on after Kansas City defender Aurelien Collin, chasing Brazilian striker Gilberto after a deft through ball from Bradley, appeared to clip the Brazilian's leg.
Gilberto, who had a clear path on goal, went down and Bradley went after the referee imploring for a call, which should have garnered Collin a red card. The French defender went unpunished and Toronto got the first four yellows of the night.
"Collin should have been sent off. I mean an under-12 ref can pick that one," Nelsen said with disgust. "That's pretty basic."
Kansas City coach Peter Vermes had a different view of the officiating.
"I thought the referee did a good job tonight, that is my personal opinion," he said. "I don't think it was an easy game to ref.
"I really liked his management of the game, the things that you can control the ball going out of bounds and the guy trying to steal 15 yards. Those are the things that drive us nuts as coaches, the little calls you might miss or might get, but those things he did a good job of and kept the game going on both sides.
Toronto hit the woodwork twice in the first half.
Follow @NeilMDavidson on TwitterSuggest a correction