The Shrimpers should have gone ahead after 26 minutes but Andrew Fleming contrived to shoot wide with the goal gaping after good work by Jack Redshaw.
It was Wimbledon who took the lead through Kevin Sainte-Luce in the 38th minute after a lovely flowing move. Rashid Yussuff played Gary Alexander in behind the visitor's defence and the latter's left-wing cross was bundled home by 19-year-old Sainte-Luce from four yards out.
The hosts doubled their advantage six minutes later from the penalty spot when Chris McCready handled a powerful Alexander effort. Jack Midson stepped up and his spot-kick into the bottom left-hand corner sent Morecambe goalkeeper Barry Roche the wrong way.
Bentley cut a frustrated figure after the game, questioning the referee's decision that led to the penalty on the stroke of half-time.
"We started brightly, we played some fantastic stuff and we should have taken the lead," said Bentley.
"After the whole week's preparation and the hundreds of miles we've travelled down to Wimbledon we just wanted a fair crack of the whip and we haven't got that.
"I don't want to say too much because referees and officials have got a hard job to do, but the result has been caused by two poor decisions. That's the be all and end all.
"I'm massively disappointed because I think we deserved something out of the game. All our hard work has been undone by two decisions that were out of our control, and that makes the journey home a bit longer. It's probably the lowest I've felt after a game."