The on-loan forward was excluded from the FA Cup semi-final defeat on Saturday after reportedly arriving late for training during the week
The Dutch forward was left out of the squad for the 2-1 loss at Wembley, with family reasons initially understood to be the cause of his exclusion.
However, reports emerged on Sunday morning suggesting the on-loan Real Madrid winger had arrived late for training during the week.
"Royston Drenthe has been the subject of a disciplinary matter," an Everton spokesman said.
"This has been dealt with internally and the club will be making no further comment."
Everton had led the semi-final through a first half Nikica Jelavic goal, but a Luis Suarez strike and a late Andy Carroll header saw Liverpool come from behind to win.
Drenthe had been involved in every round of the competition prior to the semi-final, scoring against Blackpool in the first minute to help his side into the quarter-finals.