Crabtree, the 10th overall pick in 2009 NFL Draft, has missed his third consecutive preseason, this time while nursing a left foot injury. He was placed the PUP list on July 28.
Team spokesman Bob Lange said the 49ers immediately reported the "oversight" to the league office after it happened Monday afternoon. It's unclear if the team will be penalized.
NFL spokesman Greg Aiello said the league was investigating the situation.
"We are looking into it. We appreciate Trent Baalke contacting our office to report what happened," Aiello said in an e-mail. "Our understanding is that it occurred during warm-ups and that Michael Crabtree did not participate in practice."
Crabtree hurt his foot during workouts led by Smith in June during the NFL lockout. He missed the 2010 preseason with a neck injury one year after a 71-day contract stalemate as a rookie.
Crabtree, 23, hasn't talked to reporters so far this preseason. He made 55 catches for 741 yards and six touchdowns last season, when San Francisco went 6-10. Crabtree was angrily confronted by tight end Vernon Davis during an early September practice last year, and then-coach Mike Singletary had to step between them.