Alaphilippe was thrown from his bike with 35 km to go after he collided with a motorbike which had slowed in front of a breakaway group which also included Wout van Aert of Jumbo Visma and eventual race winner Mathieu van der Poel of Alpecin-Fenix.
"That motorbike had no business being there," Lefevere told Belgian broadcaster Sporza
"Those bikes had to be on the outside by the way, because it was a slight right turn. A driver always looks for the shortest route, so he drives past there.
“Wout van Aert would not have thought that this would happen. You saw that Mathieu van der Poel was shocked that those two motos were there. He could only just avoid that motorbike, but Alaphilippe could not.”
Deceuninck-Quick-step's injured star Remco Evenepoel pulled no punches in his take of the incident.
"F***ing s**t motorbike!!!”, the 20-year-old rider tweeted.
Team sports director Brian Holm was another who took aim at the motorbike rider on Twitter, before deleting his post.
“The roadway must be cleared of spectators, motorcycles and cars,” he said.
“The last thing a tired rider and unconcentrated rider must be able to hit is a vehicle, where the pilot snores, nothing else should take the bike race or the riders’ line!”
Alaphilippe was treated on the scene after the crash before he taken to hospital.
X-rays revealed the Frenchman had suffered two fractures in his right hand and will he undergo surgery on Tuesday (AEDT)
Alaphilippe was one of the primary contenders at this year's Tour of Flanders with the race win eventually going to Van der Poel, who beat Van Aert in the sprint.