The Spanish midfielder was charged for his behaviour after the cup fifth round clash, where he entered the pitch and got into a spat with Hull assistant.
"Such a big thing has been made of that story that they go further. I know how it works at the FA. I know them for long enough," Wenger was quoted as saying by Sky Sports.
"I believe he has been charged with improper conduct for going on the pitch. Nobody told me you could be charged for that."
The French tactician added that Arsenal have a video footage of the incident, which should clear his skipper from any charges.
"I show you the tape, you watch the tape, you will be surprised he is charged. He will not be banned," Wenger declared.
Both Arsenal and Fabregas have until May 12th to submit the player's clearance evidence.