As the peloton was launched at high speed towards the finish with less than 10 kilometres to go, the Orica GreenEdge team bus crossed the line but got stuck beneath the banner.
It caused organisers to move the stage finish three kilometres from the line - a decision they reversed when the bus was freed in time.
The peloton, though, had become jittery and a massive crash with four kilometres to go took dozens of riders down, including pre-race favourite Alberto Contador.
"When a bus arrives near the finish line the driver must ask the permission to cross it," finish-line manager Jean-Louis Pages told reporters.
"Since this bus was late (and others had been through the finish already) we had already lowered the banner."
Pages said the driver had not asked for authorisation to go through.
"Everybody helped out," he said. "We deflated the tyres of the bus so we could move it away as the peloton was fast approaching."
Orica GreenEdge sports director Matt White gave a different version, saying the driver had followed instructions.
"Obviously this was a really unfortunate situation. The bus was led under the finish gantry, and we took for granted that there was enough clearance. We've had this bus since we started the team, and it's the same bus we took to the Tour last year," he was quoted as saying in a team statement.
"Our bus driver was told to move forward and became lodged under the finish gantry.
"He followed all instructions in the process that followed thanks to the hard work by (the organisers) ... that allowed him to remove the bus before the finish. It was the best possible outcome given the situation."
British champion Mark Cavendish, who was held up behind the crash, told reporters: "What caused the problems was changing the finish.
"We heard on the radio with literally 5km to go that the sprint was in 2km. And then a (kilometre) later they (said), 'No, it's at the finish'.
"It's just carnage. I'm lucky I didn't come down. I was behind it. Even my team mates were a lot worse. Tony Martin's in a bit of a state. I can count myself lucky."
Germany's Martin, Cavendish's team mate at Omega Pharma-Quick Step, was among those who crashed and he was carried in a stretcher from the team bus into an ambulance.
Marc Madiot, the manager of the FDJ.fr team, hit out at Spaniard Vicente Tortajada, president of the race commissaires.
"At first there is no problem. The commissaires decide that the line has to be moved to the three-kilometre banner so we inform our riders," the Frenchman said.
"Two kilometres further, we are told that the finish will be at its original place. But in these circumstances you don't change plans. Some teams had launched sprints, the riders were already taking risks.
"The president of the commissaires didn't do his job. When we (managers, riders) make a mistake we get a fine. Well, he should get a huge fine.
"This Spaniard, whom I don't know, can go back home."
All riders were credited with the same time because of the incident.
- Sports & Recreation