Former Rovers striker Jo Kuffour was sent tumbling on both occasions, but referee Mick Russell decided against pointing to the spot.
Former Stoke City striker Ryan Brunt scored the only goal of the match with a tame looking volley from Joe Anyinsah's cross, which caught Wycombe goalkeeper Jordan Archer unsighted.
And, after his side's efforts to salvage something from the tie, Ainsworth was left ruing the two penalty decisions.
"Jo told me afterwards he thought at least one should have been given, but referees have a difficult job and sometimes decisions don't go your way," he said.
"For half an hour we were the only team in it and I was delighted with how we were playing but, after Rovers scored, a few mistakes started to creep in.
"We finished the game strongly and might easily have snatched an equaliser in a scramble at the end so overall I'm happy enough with our performance.
"I am a big admirer of John Ward, who is one of football's gentlemen, and he has them well organised and difficult to beat."