Jemal Johnson put the Dons ahead two minutes into the second half when he cut inside from the left before smashing a right-foot pile-driver into the top corner.
Jordan Rhodes equalised following a goal-mouth scramble in the 55th minute before Jermaine Easter put the Dons 2-1 up with a cool one-on-one finish.
Theo Robinson fired in Anthony Pilkington's cross-shot on the hour mark to bring Huddersfield level again before Anthony Kay nipped in ahead of Dons keeper Willy Gueret to head the winner in the 78th minute.
"I'm disappointed and frustrated. I feel sorry for the players because they gave it a real go second half. It was individual mistakes that cost us. They had three chances and scored three goals," said Ince.
"We all know you are at your most vulnerable when you have just scored and a lack of concentration cost us twice. We were disappointed with the third goal because we had complained that they had been blocking Luke Howell at set-pieces, and that's what happened."