The Bulldogs were just 12 points down at the 12-minute mark of the final term and had momentum when Tom Liberatore tackled Brendon Goddard at half-forward, winning a free kick.
The ball spilled loose and Nathan Hrovat swooped, running in and slotting a goal that would have put his team within six points.
However, the umpire ruled that Liberatore had to take his kick, and that the goal would not count.
The Bombers kicked the next three goals to seal the game.
"I don't know why the decision was called, I honestly don't – there was a lot happening at the time," McCartney said.
"It just seemed a little surprising."
Instead of at least partially attributing the loss to the umpire's decision, the Bulldogs coach credited Essendon for steadying every time his team challenged.
"It seemed a couple of times today that just when we needed an ounce of luck, we didn't get it," McCartney said.
"But for all that, whenever we got a bit of momentum, they were good enough to do something about it and kick a goal, and that's why they're a very good team, and that's why we've still got a bit of work to go."
Hrovat, 19, also expressed surprise at the decision not to award the goal.
"I honestly don't know why it wasn't called advantage," he said.
"I think a lot of players out on the ground, including Essendon players, didn't know.
"But I guess the umpire had his reasons to bring it back, and that's the game.
"The umpire is there to do his job, and I guess you can't do much about it."
McCartney said there were positives to be taken from the Bulldogs' performance, in which they came from 37 points down during the first quarter to draw within two goals at various stages, without ever getting closer.
But he challenged his group of maturing players to start having a greater impact.
"It was a good effort," he said.
"Full credit to them – whenever we challenged them they were good enough to kick an easy one.
"No doubt that's the next stage for us, because we just work so hard at times and make hard work of opportunities.
"But we think our boys that are just getting up to 50 games now, their next 50 games have to progress a lot quicker, so that they have more influence.
"Once you've had your apprenticeship and maturity arises, you've got to produce."
The Bulldogs team on Sunday contained six players with between 30 and 60 games of experience: Tom Liberatore, who was a standout with 32 disposals, Luke Dahlhaus, Mitch Wallis, Liam Jones, Jordan Roughead and Clay Smith.
Smith suffered a suspected ruptured anterior cruciate ligament late in the game.
