Weneger was adamant that referee Martin Atkinson failed to give a foul on Francis Coquelin in the build-up to Mata's opener.
The Arsenal boss also feels that Ramires could have been booked for diving after the Blues were awarded a spot kick when the Brazilian midfielder tangled with Wojciech Szczesny.
He told reporters: "The referee gave many free kicks today. Some were much less than the Coquelin one, it's frustrating.
"It doesn't mean that we should have conceded the goal, but it's frustrating because in the big games, these kind of decisions have big importance.
"He could have given Ramires a yellow card for the penalty as well."
Arsenal are now seven points adrift of a Champions League spot in sixth place.