The second charge is for using threatening words and/or behaviour towards a Match Official.
Prutton has made a public apology for his actions: "I haven't got a leg to stand on," he told Sky Sports News.
"I've looked at it, I've thought about it and I've read about it.
"It's an horrendous situation which I've never found myself in before and, hopefully, never will again.
"I need to apologise, firstly to the ref, who was only doing his job, and to the linesman, who was only doing his job.
"Pires, I thought, had made a meal of it but, with hindsight, I've seen the pictures and heard about what happened to his leg so I'm incredibly sorry about that.
"I would never go onto the pitch to try and hurt anyone else because I wouldn't expect anyone to do it to me.
"I apologise to the people that saw it. Football nowadays, you get a lot of kids and families going. They don't pay their money to see that kind of thing.
"I felt I'd let my friends down, the team-mates, the management and everyone in the ground too because it was just ludicrous."
The 23-year-old midfielder has until 6pm on Tuesday, 1st March to respond to the charges.