The on-loan Real Madrid midfielder, 25, was left out of manager David Moyes' 18-man party for Saturday's 2-1 Wembley defeat to Liverpool.
Reports suggested Drenthe may also cross the Merseyside divide this summer, with Reds boss Kenny Dalglish said to be weighing up a move.
An Everton spokesman said: "Royston Drenthe has been the subject of a disciplinary matter. This has been dealt with internally and the club will be making no further comment."
Holland international Drenthe has impressed in patches since joining the Toffees on loan in August, scoring four goals and laying on seven more.