The 1st leg of the League One semi-final between the two clubs at the New Den saw a number of supporters spill onto the pitch.
The FA has been assisting the Metropolitan Police with their enquiries over the invasion that happened in the wake of Neil Harris' second-half goal.
Casper Ankergren claimed to have been pushed in the back, while also having missiles thrown at him during the incident. Two supporters were then arrested in relation to the invasion.
An FA spokesperson told the Yorkshire Evening Post: "The FA has noted that two people were apprehended by stewards and arrested and charged by police. No further action from the FA is to be taken."