The German boss claimed his side should have been awarded a free-kick in the build-up to the Cherries' first goal when left-back Charlie Daniels appeared to foul Florent Hadergjonaj.
And Wagner went on to suggest Callum Wilson's second goal five minutes later also should have been ruled out for offside.
Analysing the lead-up to the opening goal, Phil Neville said: “You can criticise the referee Lee Probert but I think he needs to get help from the linesman there.
“It's a clear foul on Florent Hadergjonaj - I don't think it's a red card, it's a yellow card at most but I can't believe he did not give a foul for that.
“If he had given a foul it would have stopped the play and Callum Wilson's goal.
Alan Shearer agreed: “It should have been a foul but instead they get a corner and they score from three yards out with a free header.
“That's the first one and for the second one it should have been offside – it's a good ball into the box but Huddersfield Town have held their line well.
“The linesman should flag but he doesn't and again, it's a very good finish.”