If it were properly called, the runner from 3B's run should have counted unless and until a proper play (either while the ball was still live, or immediately after by a proper appeal) was made to get him out at third base for having left early.
Many people think of the play made, in this case, on the runner who left 2nd early as if it were a force play. It is not. It is a "time play". This means that if the other runner crosses the plate before the third out is made, the run counts. In order to get the run off the board, you would have to record an out on the runner who left third early and scored.
This is the classic "4th out" play and it is a standard item in rule trivia quizzes.
Note, however, that if the runners were not going hard, it is possible that the RF's throw to 2nd recorded the third out before a runner crossed home. If the third out occurred before the runner crossed home, there was never a run in the first place and thus, no appeal would be necessary.