Latics dominated the game in terms of possession and chances, and could easily have doubled the winning margin such was their superiority.
Marc-Antoine Fortune grabbed the opening goal after just five minutes, with an own goal from Elliott Ward and a wonder goal from Jordi Gomez completing the scoring after the break.
"We weren't at our best, I think that was pretty clear," acknowledged Howe.
"We didn't start the game very well - the real Bournemouth didn't turn up to play.
"We were under pressure, we gave the ball away in dangerous areas which is unlike us, and it was only in the last half hour when we came alive.
"The substitutes breathed new life into us and we showed we are a good side.
"But it's a feeling of of disappointment we will leave with, because we haven't given a very good account of ourselves."
Wigan were at it right from the off, and Howe was at a loss to explain why the Cherries took so long to get into the game.
"I'm not sure why we started so slowly," he added.
"We knew what to expect, that Wigan play a high, pressing game, and we prepared for that.
"But we didn't adapt very well to the demands placed upon us and we were on the back foot right from the off.
"We'll regroup now and hopefully produce a better performance against Burton in the FA Cup on Tuesday night.
"You have to learn from every defeat, and it's important we use experiences like this to move forward."
- Sports & Recreation
- Elliott Ward