The 31-year-old didn't arrive in time for the plane from Kansas City to Detroit on Monday. He arrived with the team on Tuesday after catching a different flight.
Duffy was scratched from his outing as a disciplinary measure, manager Mike Matheny said.
The pitcher is physically OK and remains on the active roster, according to Matheny, who added that Tuesday's starter is yet to be determined.
Duffy owns a 4.24 ERA and 1.22 WHIP with 47 strikeouts in 46 2/3 innings.